U.S. patent number 10,365,434 [Application Number 15/180,016] was granted by the patent office on 2019-07-30 for integrated target waveguide devices and systems for optical coupling.
This patent grant is currently assigned to Pacific Biosciences of California, Inc.. The grantee listed for this patent is Pacific Biosciences of California, Inc.. Invention is credited to Mathieu Foquet, Ariel Herrmann, Paul Lundquist, Mark McDonald, Aaron Rulison, Shang Wang.
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United States Patent |
10,365,434 |
Wang , et al. |
July 30, 2019 |
Integrated target waveguide devices and systems for optical
coupling
Abstract
Integrated target waveguide devices and optical analytical
systems comprising such devices are provided. The target devices
include an optical coupler that is optically coupled to an
integrated waveguide and that is configured to receive optical
input from an optical source through free space, particularly
through a low numerical aperture interface. The devices and systems
are useful in the analysis of highly multiplexed optical reactions
in large numbers at high densities, including biochemical
reactions, such as nucleic acid sequencing reactions. The devices
provide for the efficient and reliable coupling of optical
excitation energy from an optical source to the optical reactions.
Optical signals emitted from the reactions can thus be measured
with high sensitivity and discrimination. The devices and systems
are well suited for miniaturization and high throughput.
Inventors: |
Wang; Shang (San Carlos,
CA), Foquet; Mathieu (Newark, CA), Lundquist; Paul
(San Francisco, CA), Rulison; Aaron (Los Altos, CA),
McDonald; Mark (Milpitas, CA), Herrmann; Ariel (San
Francisco, CA) |
Applicant: |
Name |
City |
State |
Country |
Type |
Pacific Biosciences of California, Inc. |
Menlo Park |
CA |
US |
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Assignee: |
Pacific Biosciences of California,
Inc. (Menlo Park, CA)
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Family
ID: |
57504272 |
Appl.
No.: |
15/180,016 |
Filed: |
June 11, 2016 |
Prior Publication Data
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Document
Identifier |
Publication Date |
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US 20160363728 A1 |
Dec 15, 2016 |
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Related U.S. Patent Documents
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Application
Number |
Filing Date |
Patent Number |
Issue Date |
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62175139 |
Jun 12, 2015 |
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Current U.S.
Class: |
1/1 |
Current CPC
Class: |
G02B
6/124 (20130101); G01N 21/648 (20130101); G01N
21/774 (20130101); G02B 6/34 (20130101); G01N
21/03 (20130101); G01N 21/6452 (20130101); G01N
21/6486 (20130101); G02B 6/4221 (20130101); G01N
21/7703 (20130101); G02B 2006/12135 (20130101); G01N
2021/0346 (20130101) |
Current International
Class: |
G02B
6/34 (20060101); G01N 21/03 (20060101); G02B
6/124 (20060101); G01N 21/64 (20060101); G01N
21/77 (20060101); G02B 6/12 (20060101); G02B
6/42 (20060101) |
References Cited
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Primary Examiner: Doan; Jennifer
Attorney, Agent or Firm: VLP Law Group LLP
Parent Case Text
CROSS-REFERENCE TO RELATED APPLICATIONS
This application claims the benefit of U.S. Provisional Application
No. 62/175,139, filed on Jun. 12, 2015, the disclosure of which is
incorporated herein by reference in its entirety.
Claims
What is claimed is:
1. An optical analytical system comprising: an optical source; and
an integrated target waveguide device comprising a low numerical
aperture optical coupler of at least 100 .mu.m.sup.2 in size; and
an integrated waveguide optically coupled to the optical coupler;
wherein the optical source provides light of wavelength in the
range from 400 nm to 700 nm; wherein the optical source is
optically coupled to the optical coupler of the target waveguide
device through free space at a distance of at least 1 mm, and
wherein the integrated target waveguide device is removeable.
2. The optical analytical system of claim 1, wherein the optical
source has a numerical aperture of no more than 0.1.
3. The optical analytical system of claim 1, wherein the optical
source is configured to illuminate a spot on the target waveguide
device with a surface area per spot of at least 100
.mu.m.sup.2.
4. The optical analytical system of claim 1, wherein the optical
source is configured to illuminate a spot on the target waveguide
device with a surface area per spot of at most 250,000
.mu.m.sup.2.
5. The optical analytical system of claim 1, wherein the optical
source is configured to illuminate a spot on the target waveguide
device with a surface area per spot of from 100 .mu.m.sup.2 to
250,000 .mu.m.sup.2.
6. The optical analytical system of claim 5, wherein the optical
source is configured to illuminate the spot on the target waveguide
device at a distance of from 1 mm to 100 mm.
7. The optical analytical system of claim 1, wherein the optical
source is configured to illuminate a spot on the target waveguide
device with a power per spot of at least 1 mW.
8. The optical analytical system of claim 7, wherein the optical
source is configured to illuminate the spot on the target waveguide
device at a distance of from 1 mm to 100 mm.
9. The optical analytical system of claim 1, wherein the optical
source emits a plurality of light beams.
10. The optical analytical system of claim 9, wherein the optical
source emits at least four light beams.
11. The optical analytical system of claim 9, wherein the optical
source emits at least one sample excitation beam and at least one
alignment beam.
12. The optical analytical system of claim 11, wherein the
alignment beam has an alignment beam output power and the sample
excitation beam has a sample beam output power, and wherein the
alignment beam output power is lower than the sample excitation
beam output power.
13. The optical analytical system of claim 12, wherein the
alignment beam output power is no more than 10% of the sample
excitation beam output power.
14. The optical analytical system of claim 11, further comprising
an alignment detector.
15. The optical analytical system of claim 14, wherein the
alignment detector is a camera.
16. The optical analytical system of claim 1, wherein the optical
source comprises a planar lightwave circuit.
17. The optical analytical system of claim 1, wherein the optical
source provides light of wavelength in the range from 450 nm to 650
nm.
18. The optical analytical system of claim 1, further comprising a
heat sink.
19. The optical analytical system of claim 1, further comprising an
optical element, wherein the optical element is positioned between
the optical source and the target waveguide device.
20. The optical analytical system of claim 19, wherein the optical
element modulates the focus of an optical beam transmitted from the
optical source to the target waveguide device.
21. The optical analytical system of claim 19, wherein the optical
element modulates the size of an optical beam transmitted from the
optical source to the target waveguide device.
22. The optical analytical system of claim 1, wherein the optical
coupler of the target waveguide device has a numerical aperture of
no more than 0.10.
23. The optical analytical system of claim 1, wherein the optical
coupler of the target waveguide device is a grating coupler.
24. The optical analytical system of claim 1, wherein the target
waveguide device further comprises a reflective layer positioned
below the optical coupler.
25. The optical analytical system of claim 1, wherein the target
waveguide device further comprises a heat spreading layer in
thermal contact with the optical coupler.
26. The optical analytical system of claim 1, wherein the target
waveguide device further comprises an alignment feature.
27. The optical analytical system of claim 1, wherein the target
waveguide device comprises a plurality of optical couplers and a
plurality of integrated waveguides optically coupled to the
plurality of optical couplers.
28. The optical analytical system of claim 1, wherein the target
waveguide device further comprises a plurality of nanoscale sample
wells optically coupled to the integrated waveguide.
Description
BACKGROUND OF THE INVENTION
As multiplexed optical analytical systems continue to be
miniaturized in size, expanded in scale, and increased in power,
the need to develop improved systems capable of delivering optical
energy to such systems becomes more important. For example, highly
multiplexed analytical systems comprising integrated waveguides for
the illumination of nanoscale samples are described in U.S. Patent
Application Publication Nos. 2008/0128627 and 2012/0085894. Further
optical systems for the analysis of nanoscale samples, including
the illumination and detection of such samples, are described in
U.S. Patent Application Publication Nos. 2012/0014837,
2012/0021525, and 2012/0019828. Additional nanoscale illumination
systems for highly multiplexed analysis are described in U.S.
Patent Application Publication Nos. 2014/0199016 and
2014/0287964.
In conventional optical systems, optical trains are typically
employed to direct, focus, filter, split, separate, and detect
light to and from the sample materials. Such systems typically
employ an assortment of different optical elements to direct,
modify, and otherwise manipulate light entering and leaving a
reaction site. Such systems are frequently complex and costly and
tend to have significant space requirements. For example, typical
systems employ mirrors and prisms in directing light from its
source to a desired destination. Additionally, such systems can
include light-splitting optics such as beam-splitting prisms to
generate two or more beams from a single original beam.
Alternatives to the conventional optical systems have been
described, in particular alternative systems having integrated
optical components designed and fabricated within highly confined
environments. For example, planar lightwave circuits (PLCs)
comprising fiber interfaces, wavelength filters or combiners,
phase-delayed optical interferometers, optical isolators,
polarization control, and/or taps have been developed for use in
telecommunications applications. In some cases these devices
additionally include one or more laser sources and one or more
optical detectors. The devices, which are sometimes also referred
to as fiber spacing concentrators (FSCs), use integrated optical
waveguides to route photons through an optical circuit, in much the
same way as electrons are routed through an electrical circuit.
They are fabricated using standard semiconductor fabrication
techniques, and they can accordingly integrate both passive
components, such as optical filters and fiber pigtail connectors,
and active elements, such as optical switches and attenuators,
during the fabrication process. As used in telecommunications
equipment, they typically serve to couple and/or split optical
signals from fiber optic cores, for the purpose of, for example,
multiplexing/demultiplexing, optical branching, and/or optical
switching. The devices thus provide the functionality of a more
traditional optical train, while at the same time being
significantly less expensive, more compact, and more robust.
In the just-described optical systems, an optical source and its
target device are typically closely and permanently associated with
one another within the system. For example, PLCs used in
telecommunications applications are typically mechanically aligned
and bonded to their laser light source and to their associated
photodetectors during the manufacturing process. Such close and
irreversible associations between an optical source and its target
device are thus not well suited for use in analytical systems
having a removable sample holder, where the optical output from an
optical source, such as a traditional optical train, is normally
coupled to the target sample holder through free space. In systems
optically coupled through free space, the optical signal from an
optical source needs to be aligned with a target device each time
the target device is replaced, and the alignment can even need to
be monitored and maintained during the course of an analysis, due
to mechanical, thermal, and other interfering factors associated
with the optical system. In addition, the integrated optical
circuits typically used in telecommunications applications are not
designed to carry the intensity of optical energy necessary to
analyze the large numbers of nanoscale samples present in the
highly-multiplexed analytical systems described above, nor are they
designed for use with optical sources having wavelengths suitable
for use in optical systems with standard biological reagents.
Another consideration in the design of an optical analytical system
is the method of coupling of light from the optical source into the
target device. For example, where a target device comprises an
integrated optical waveguide for routing the optical energy through
the device, launching of the optical energy into the waveguide can
be unreliable and inefficient. Various optical couplers have been
described to achieve this purpose, including the use of direct
"endfire" coupling into a polished end of the waveguide, the use of
a prism coupler to direct light into the waveguide, and the use of
a grating coupler to direct light into the waveguide. Depending on
the implementation, however, each approach has limitations with
respect to efficiency, reliability, applicability, cost, and the
like.
There is thus a continuing need to improve the performance and
properties of integrated optical waveguide devices, particularly
those that are reversibly coupled to external light sources. There
is also a need to improve the performance and properties of optical
analytical systems containing such integrated waveguide
devices.
SUMMARY OF THE INVENTION
The present disclosure addresses these and other needs by providing
in one aspect an integrated target waveguide device comprising an
optical coupler and an integrated waveguide optically coupled to
the optical coupler. In this device, the optical coupler is a low
numerical aperture coupler and is at least 100 .mu.m.sup.2 in
size.
In another aspect, the disclosure provides an integrated target
waveguide device comprising an optical coupler, an integrated
waveguide optically coupled to the optical coupler, and at least
one alignment feature. In this device, the optical coupler is also
a low numerical aperture coupler and is also at least 100
.mu.m.sup.2 in size.
In yet another aspect, the disclosure provides an optical
analytical system comprising an optical source and any of the
integrated target waveguide devices disclosed herein. In this
system, the optical source is optically coupled to the optical
coupler of the target waveguide device through free space at a
distance of at least 1 mm.
BRIEF DESCRIPTION OF THE DRAWINGS
FIGS. 1A-1C illustrate differences between coupling from an optical
source with high numerical aperture, such as a fiber tip, and
coupling from an optical source with low numerical aperture through
free space to a target waveguide device.
FIG. 2A shows a plot of the intensity of a Gaussian beam as a
function of distance from the beam axis. FIG. 2B illustrates the
shape of a divergent Gaussian beam of radius w(z).
FIG. 3A shows the basic design features and structure of a standard
grating coupler, and FIG. 3B shows the same for a blazed grating
coupler. FIGS. 3C to 3L show alternative optical grating coupler
designs and structural features.
FIG. 4A shows the input coupling region of an exemplary target
waveguide device with active waveguide alignment features. FIG. 4B
shows in closer detail the two types of input couplers used in the
waveguide device of FIG. 4A. FIG. 4C shows another exemplary input
coupling region that includes both waveguide alignment features and
patterned region alignment features. FIG. 4D shows the top view of
an exemplary integrated target waveguide device, including the
input coupling region, routing paths, fanout regions, and the
arrayed nanoscale sample region. FIG. 4E shows an exemplary optical
analytical system, including an optical source comprising lasers, a
beam power controller, and a "light brush" to direct the optical
input to the integrated target waveguide device. Also shown is an
alignment camera. FIG. 4F shows the degrees of freedom to be
controlled during the alignment of an optical source and a target
device. The motions are designated along track (AT), cross track
(CT), pitch, yaw, and roll (or pattern rotation). Not shown is
movement in the up-down dimension.
FIGS. 5A-5D illustrate exemplary grating couplers. FIG. 5A shows a
basic grating coupler. FIG. 5B shows a structure that includes an
optical reflective layer directly below the coupler. FIG. 5C shows
a structure with a heat spreading layer directly below the coupler.
FIG. 5D shows a structure with both a reflective layer and a heat
spreading layer below the coupler.
FIG. 6 illustrates "hotspots" created by a multimode coupler.
FIG. 7 shows the effect of linear polarized excitation light on
targets at different locations in a nanowell/ZMW.
FIG. 8 shows the effect of circular polarized excitation light on
targets at different locations in a nanowell/ZMW
FIG. 9 shows the effect of excitation with different TE modes on
targets at different locations in a nanowell/ZMW.
FIG. 10 shows the pattern of TE, TM, and TEM modes in a rectangular
waveguide
FIGS. 11A-11B illustrate single-look and multi-look coupling with
grating-coupled waveguide devices (A) and endfire-coupled waveguide
devices (B).
FIGS. 12A-12C illustrate single-look (A) and multi-look (B and C)
devices configured for illumination by three separate input optical
beams. The devices include input grating couplers (A and B) or
endfire couplers (C).
FIG. 13 illustrates the use of thermal Mach-Zehnder switches to
control multi-look illumination in an endfire-coupled target
device.
FIG. 14A shows an instrument-level implementation of a
polarization-based 2-look system. FIG. 14B shows a device-level
implementation of a polarization-based 2-look system.
FIG. 15 illustrates the use of an arrayed waveguide grating (AWG)
to tune excitation wavelengths for multi-look reactions.
FIG. 16 shows a novel fiber spacing concentrator with active core
alignment.
FIG. 17A illustrates a 2-dimensional low-NA grating coupler model.
FIG. 17B illustrates the modeled optical energy coupled through the
device into an integrated waveguide, where the optical energy is
directed from the middle of the device towards the left side of the
device.
FIG. 18 provides a comparison of coupling efficiencies for various
binary grating coupler designs.
FIG. 19 provides a comparison of coupling efficiencies for various
binary grating coupler designs with different numerical aperture
values.
FIG. 20 illustrates fiber-to-grating alignment tolerances at
various numerical aperture values.
FIGS. 21A-21D illustrate the impact of grating period (A), buried
oxide cladding thickness (B), duty cycle (C), and etch depth (D) on
coupling efficiency at various numerical aperture values.
FIG. 22 summarizes the simulated efficiencies of exemplary couplers
designed and simulated using the parameters shown.
FIG. 23A shows the cross section of an exemplary waveguide of the
instant target devices, and FIG. 23B shows the electric field
intensity through the center of the waveguide.
FIG. 24 shows mode profiles for prototype coupled waveguide
devices.
FIG. 25 illustrates the impact of y misalignment on the efficiency
of coupling.
FIG. 26 illustrates the relationship between the prism refractive
index and the input incident angle for a prism-coupled device.
FIG. 27 illustrates the relationship between the grating period and
the input incident angle for a grating-coupled device.
FIG. 28 shows the experimental setup used to test the effectiveness
of a heat-spreading layer in mitigating laser-induced thermal
damage.
FIGS. 29A-29G show the results of testing samples containing a
heat-spreading layer.
FIG. 30 shows simulations of optimized waveguide dimensions for
single-mode operation in two different waveguide cores with 552 nm
light.
FIG. 31 shows the Gaussian profile for a simulated input beam
source.
FIGS. 32A-32B illustrate a 2-dimensional grating coupler model for
a target waveguide device and the modeled optical energy coupled
through the device into an integrated waveguide.
FIG. 33 illustrates effects of wavelength on modeled coupling
efficiency for a high NA grating coupler design with a titanium
dioxide core.
FIGS. 34A-34B illustrate effects of grating coupler period on
modeled coupling efficiency for a high NA grating coupler design
with a titanium dioxide core and a 552 nm input source.
FIGS. 35A-35B illustrate effects of grating coupler duty cycle on
modeled coupling efficiency for a high NA grating coupler design
with a titanium dioxide core and a 552 nm input source.
FIGS. 36A-36B illustrate effects of grating coupler etch depth on
modeled coupling efficiency for a high NA grating coupler design
with a titanium dioxide core and a 552 nm input source.
FIGS. 37A-37B illustrate effects of reflector distance on modeled
coupling efficiency for a high NA grating coupler design with a
titanium dioxide core and a 552 nm input source.
FIGS. 38A-38B illustrate effects of top clad thickness on modeled
coupling efficiency for a high NA grating coupler design with a
titanium dioxide core and a 552 nm input source.
FIGS. 39A-39B illustrate effects of waveguide core index on modeled
coupling efficiency for a high NA grating coupler design with a
titanium dioxide core and a 552 nm input source.
FIG. 40 plots modeled coupling efficiency for a high NA grating
coupler design with a titanium dioxide core and a 532 nm input
source.
FIGS. 41A-41B illustrate effects of grating coupler period on
modeled coupling efficiency for a high NA grating coupler design
with a titanium dioxide core and a 532 nm input source.
FIGS. 42A-42B illustrate effects of grating coupler duty cycle on
modeled coupling efficiency for a high NA grating coupler design
with a titanium dioxide core and a 532 nm input source.
FIGS. 43A-43B illustrate effects of grating coupler etch depth on
modeled coupling efficiency for a high NA grating coupler design
with a titanium dioxide core and a 532 nm input source.
FIGS. 44A-44B illustrate effects of reflector distance on modeled
coupling efficiency for a high NA grating coupler design with a
titanium dioxide core and a 532 nm input source.
FIGS. 45A-45B illustrate effects of top clad thickness on modeled
coupling efficiency for a high NA grating coupler design with a
titanium dioxide core and a 532 nm input source.
DETAILED DESCRIPTION OF THE INVENTION
Optical Analytical Systems
Multiplexed optical analytical systems are used in a wide variety
of different applications. Such applications can include the
analysis of single molecules, and can involve observing, for
example, single biomolecules in real time as they interact with one
another. For ease of discussion, such multiplexed systems are
discussed herein in terms of a preferred application: the analysis
of nucleic acid sequence information, and particularly, in
single-molecule nucleic acid sequence analysis. Although described
in terms of a particular application, however, it should be
appreciated that the devices and systems described herein are of
broader application.
In the context of single-molecule nucleic acid sequencing analyses,
a single immobilized nucleic acid synthesis complex, comprising a
polymerase enzyme, a template nucleic acid whose sequence is being
elucidated, and a primer sequence that is complementary to a
portion of the template sequence, is observed analytically in order
to identify individual nucleotides as they are incorporated into
the extended primer sequence. Incorporation is typically monitored
by observing an optically detectable label on the nucleotide, prior
to, during, or following its incorporation into the extended
primer. In some cases, such single molecule analyses employ a "one
base at a time approach", whereby a single type of labeled
nucleotide is introduced to and contacted with the complex at a
time. In some cases, unincorporated nucleotides are washed away
from the complex following the reaction, and the labeled
incorporated nucleotides are detected as a part of the immobilized
complex. In other cases, it is possible to monitor the
incorporation of nucleotides in real time without washing away
unincorporated nucleotides.
In order to obtain the volumes of sequence information that can be
desired for the widespread application of genetic sequencing, e.g.,
in research and diagnostics, higher throughput systems are desired.
By way of example, in order to enhance the sequencing throughput of
the system, multiple complexes are typically monitored, where each
complex sequences a separate DNA template. In the case of genomic
sequencing or sequencing of other large DNA components, these
templates typically comprise overlapping fragments of genomic DNA.
By sequencing each fragment, a contiguous sequence can thus be
assembled using the overlapping sequence data from the separate
fragments.
A single template/DNA polymerase-primer complex of such a
sequencing system can be provided, typically immobilized, within a
nanoscale, optically-confined region on or near the surface of a
transparent substrate, optical waveguide, or the like. Such an
approach is described in U.S. Pat. No. 7,056,661, which is
incorporated by reference herein in its entirety. These
optically-confined regions are preferably fabricated as nanoscale
sample wells, also known as nanoscale reaction wells, nanowells, or
zero mode waveguides (ZMWs), in large arrays on a suitable
substrate in order to achieve the scale necessary for genomic or
other large-scale DNA sequencing approaches. Such arrays preferably
also include an associated optical source or sources, to provide
excitation energy, an associated emission detector or detectors, to
collect optical energy emitted from the samples, and associated
electronics. Together, the components thus comprise a fully
operational optical analytical device or system. Examples of
analytical devices and systems useful in single-molecule nucleic
acid sequence analysis include those described in U.S. Pat. Nos.
6,917,726, 7,170,050, and 7,935,310; U.S. Patent Application
Publication Nos. 2012/0014837, 2012/0019828, and 2012/0021525; and
U.S. patent application Ser. No. 13/920,037, which are each
incorporated by reference herein in their entireties.
In embodiments, the instant optical analytical systems comprise an
optical source that is coupled to a target device, typically an
integrated target waveguide device. As will be described in more
detail below, the optical source and the associated target device
are configured for efficient coupling through free space, for
example at a distance of at least 1 mm, at least 2 mm, at least 3
mm, at least 5 mm, at least 10 mm, at least 20 mm, at least 30 mm,
at least 50 mm, or even at least 100 mm.
As will also be described in more detail below, it can be
advantageous in the efficient coupling of optical energy from the
optical source to the target device for the optical devices to be
configured with low numerical aperture. By "low numerical aperture"
it is meant that the numerical aperture is lower than the numerical
aperture of near-field coupled optical devices. Specifically, it is
meant that the numerical aperture is no more than 0.1. Accordingly,
in some system embodiments, the optical source and the associated
target device have numerical apertures of no more than 0.1, no more
than 0.08, no more than 0.05, no more than 0.03, no more than 0.02,
or even no more than 0.01. Furthermore, in some embodiments, the
optical source is configured to illuminate a spot on the associated
target device with a surface area per spot of at least 100
.mu.m.sup.2, at least 144 .mu.m.sup.2, at least 225 .mu.m.sup.2, at
least 400 .mu.m.sup.2, at least 625 .mu.m.sup.2, at least 900
.mu.m.sup.2, at least 1600 .mu.m.sup.2, at least 2500 .mu.m.sup.2,
at least 4900 .mu.m.sup.2, at least 10,000 .mu.m.sup.2, or even
higher. In other embodiments, the optical source is configured to
illuminate a spot on the associated target device with a surface
area per spot of at most 250,000 .mu.m.sup.2, at most 62,500
.mu.m.sup.2, at most 22,500 .mu.m.sup.2, at most 10,000
.mu.m.sup.2, at most 6400 .mu.m.sup.2, at most 3600 .mu.m.sup.2, or
at most 2500 .mu.m.sup.2. In still other embodiments, the optical
source is configured to illuminate a spot on the associated target
device with a surface area per spot of from 100 .mu.m.sup.2 to
250,000 .mu.m.sup.2, from 225 .mu.m.sup.2 to 62,500 .mu.m.sup.2,
from 400 .mu.m.sup.2 to 22,500 .mu.m.sup.2, from 625 .mu.m.sup.2 to
10,000 .mu.m.sup.2, from 900 .mu.m.sup.2 to 6400 .mu.m.sup.2, or
even from 1600 .mu.m.sup.2 to 3600 .mu.m.sup.2.
In some system embodiments, the optical source is configured to
illuminate a spot on the associated target device with a power of
at least 1 mW, at least 2 mW, at least 3 mW, at least 5 mW, at
least 10 mW, at least 20 mW, at least 30 mW, at least 50 mW, or at
least 100 mW per spot.
In some system embodiments, the optical source emits a plurality of
light beams. The separate light beams are preferably arranged to
illuminate a corresponding plurality of optical input couplers on
the associated target device. Separating the optical energy into
multiple beams can be advantageous in decreasing the input energy
per beam and thus decreasing the requirement to dissipate heat
energy on the target device. In some embodiments, the optical
source emits at least four light beams. In specific embodiments,
the optical source emits at least eight light beams or even at
least twelve light beams.
In some embodiments, the optical source emits at least one sample
excitation beam and at least one alignment beam. As will be
described in more detail below, the sample excitation beam is
directed through free space to an input coupler on the target
waveguide device and from there is directed--typically through an
array of integrated waveguides--to nanoscale sample wells arrayed
on the device. The alignment beam is directed through free space to
an alignment feature on the target waveguide device and serves to
align the target device and the optical source or to maintain such
alignment, as will be described in further detail below. In
specific embodiments, the alignment beam is of a lower output power
than the sample excitation beam. In some embodiments, the alignment
beam has no more than 10% of the output power of the sample
excitation beam. More specifically, the alignment beam has no more
than 5% of the output power of the sample excitation beam or even
no more than 1% of the output power of the sample excitation
beam.
Accordingly, in some system embodiments, the target device
comprises an alignment feature, and the optical system further
comprises an alignment detector. The combination of an alignment
feature on the target device and an alignment light beam and
alignment detector within the system is particularly useful in
systems where the target device is designed to be removable. In
such a system, when a new target device is installed into the
system, the alignment feature or features on the target device can
be used by the alignment detector to adjust the position of the
target device relative to other components of the system,
particularly with respect to the optical source, and can thus
optimize the coupling of optical energy from the optical source to
the target device.
For example, in systems where the optical source emits multiple
optical beams, such as in some of the integrated optical delivery
devices described in co-owned U.S. Patent Application No.
62/133,965, filed on Mar. 16, 2015, and U.S. patent application
Ser. No. 15/072,146, filed on Mar. 16, 2016, the disclosures of
which are incorporated by reference herein in their entireties, it
can be difficult to achieve optimal alignment of the multiple beams
with the multiple input couplers of a target device and to maintain
that alignment during the course of a measurement. The alignment
beams and associated alignment features of the instant systems
overcome those difficulties both by facilitating the initial
alignment of the optical source and the target device within the
optical system and by maintaining that alignment during the course
of an analytical assay.
In particular, the process of aligning an optical source with the
target device can include a coarse alignment process, a fine
alignment process, or both coarse and fine alignment processes.
During the alignment process, the target waveguide device itself
can be moved relative to the optical source, the optical source can
be moved relative to the target waveguide device, or both devices
can be moved relative to one another. In preferred system
embodiments, the alignment detector provides for the dynamic
alignment of the integrated target waveguide device and the optical
source, such that alignment between the components is maintained
during an assay. In some system embodiments, the alignment detector
is a camera.
As was described in U.S. Patent Application No. 62/133,965 and Ser.
No. 15/072,146, the optical source of the instant systems can
provide a modulated optical signal. In specific embodiments, the
modulated optical signal can be amplitude modulated, phase
modulated, frequency modulated, or a combination of such
modulations.
In certain embodiments, the optical source of the instant optical
systems is one or more lasers, including vertical-cavity
surface-emitting lasers, one or more light-emitting diodes, or one
or more other comparable optical devices. In specific embodiments,
the optical source is one or more lasers.
As already noted, in the analysis of genomic sequence information,
it can be advantageous for the target devices of the instant
optical analytical systems to include arrays with large numbers of
nanoscale sample wells. In order to achieve such scale, the arrays
can be fabricated at ultra-high density, providing anywhere from
1000 nanowells per cm.sup.2, to 10,000,000 nanowells per cm.sup.2,
or even higher density. Thus, at any given time, it can be
desirable to analyze the reactions occurring in 100, 1000, 3000,
5000, 10,000, 20,000, 50,000, 100,000, 1 Million, 5 Million, 10
Million, or even more nanowells or other sample regions within a
single analytical system, and preferably on a single suitable
substrate.
In order to achieve the ultra-high density of nanowells necessary
for such arrays, the dimensions of each nanowell must be relatively
small. For example, the length and width of each nanowell is
typically in the range of from 50 nm to 600 nm, ideally in the
range of from 100 nm to 300 nm. It should be understood that
smaller dimensions allow the use of smaller volumes of reagents and
can, in some cases, help to minimize background signals from
reagents outside the reaction zone and/or outside the illumination
volume. Accordingly, in some embodiments, the depth of the nanowell
can be in the range of 50 nm to 600 nm, more ideally in the range
of 100 nm to 500 nm, or even more ideally in the range of 150 to
300 nm.
It should also be understood that the shape of a nanowell will be
chosen according to the desired properties and methods of
fabrication. For example, the shape of the nanowell can be
circular, elliptical, square, rectangular, or any other desired
shape. Furthermore, the walls of the nanowell can be fabricated to
be vertical, or the walls of the nanowell can be fabricated to
slope inward or outward if so desired. In the case of a circular
nanowell, an inward or outward slope would result in, for example,
a cone-shaped or inverted cone-shaped nanowell.
Using the foregoing systems, simultaneous targeted illumination of
thousands, tens of thousands, hundreds of thousands, millions, or
even tens of millions of nanowells in an array is possible. As the
desire for multiplex increases, and as the density of nanowells on
an array accordingly increases, the ability to provide targeted
illumination of such arrays also increases in difficulty, as issues
of nanowell cross-talk (signals from neighboring nanowells
contaminating each other as they exit the array), decreased
signal:noise ratios and increased requirements for dissipation of
thermal energy at higher levels of denser illumination, and the
like, increase. The target waveguide devices and optical analytical
systems of the instant specification address some of these issues
by providing improved illumination of the waveguides optically
coupled to the arrayed nanowells.
Accordingly, the instant disclosure provides optical analytical
systems comprising an optical source, such as a laser or another
suitable optical source, and an integrated target waveguide device,
such as a multiplexed integrated DNA sequencing chip, where the
optical source and the target device are optically coupled to one
another.
In some system embodiments, particularly where, as described below,
the target waveguide device comprises a heat spreading layer, the
instant optical analytical systems further comprise a heat sink,
wherein the heat sink is in thermal contact with the heat spreading
layer of the target device. The heat sink thus receives thermal
energy from the heat spreading layer and thereby prevents the
optical couplers on the target device from overheating. Such a heat
sink may optionally contain fins or the like, in order to maximize
surface area and thus heat exchange with the surrounding
environment. The heat sink may alternatively, or in addition,
contain a refrigerant, or other appropriate liquid, to further
improve the efficiency and heat capacity of the device. The heat
sink may optionally still further include a fan or other such
circulating device for still further improvement of thermal
transfer.
Target Waveguide Devices
As mentioned above, the optical analytical systems of the instant
specification comprise a target device that, in some embodiments,
comprises a plurality of integrated optical waveguides to deliver
excitation energy to an array of samples within the device. The use
of integrated optical waveguides to deliver excitation illumination
is advantageous for numerous reasons. For example, because the
illumination light is applied in a spatially focused manner, e.g.,
confined in at least one lateral and one orthogonal dimension,
using efficient optical systems, e.g., fiber optics, waveguides,
multilayer dielectric stacks (e.g., dielectric reflectors), etc.,
the approach provides an efficient use of illumination (e.g.,
laser) power. For example, illumination of a device comprising an
array of nanowells using waveguide arrays as described herein can
reduce the illumination power .about.10- to 1000-fold as compared
to illumination of the same substrate using a free space
illumination scheme comprising, for example, separate illumination
(e.g., via laser beams) of each reaction site. In general, the
higher the multiplex (i.e., the more surface regions to be
illuminated on the substrate), the greater the potential energy
savings offered by waveguide illumination. In addition, if the
optical energy, for example from a laser source, is efficiently
coupled into the optical analytical system, waveguide illumination
need not pass through a free space optical train prior to reaching
the surface region to be illuminated, and the illumination power
can be further reduced.
In addition, because illumination of samples is provided from
within the confined regions of the target device itself (e.g.,
optical waveguides), issues of illumination of background or
non-relevant regions, e.g., illumination of non-relevant materials
in solutions, autofluorescence of substrates, and/or other
materials, reflection of illumination radiation, etc., are
substantially reduced.
In addition to mitigating autofluorescence of substrate materials
within a target device, the coupling of excitation illumination to
integrated waveguides can substantially mitigate autofluorescence
associated with an optical train. In particular, in typical
fluorescence spectroscopy, excitation light is directed at a
reaction of interest through at least a portion of the same optical
train used to collect signal fluorescence, e.g., the objective and
other optical train components. As such, autofluorescence of such
components will contribute to the detected fluorescence level and
can provide signal noise in the overall detection. Because the
systems provided herein typically direct excitation light into the
device through a different path, e.g., through a grating coupler,
or the like, optically connected to the waveguide in the target
device, this source of autofluorescence is eliminated.
Waveguide-mediated illumination is also advantageous with respect
to alignment of illumination light with surface regions to be
illuminated. In particular, substrate-based analytical systems, and
particularly those that rely upon fluorescent or fluorogenic
signals for the monitoring of reactions, typically employ
illumination schemes whereby each analyte region must be
illuminated by optical energy of an appropriate wavelength, e.g.,
excitation illumination. While bathing or flooding the substrate
with excitation illumination serves to illuminate large numbers of
discrete regions, such illumination may suffer from the myriad
complications described above. To address those issues, targeted
excitation illumination can serve to selectively direct separate
beams of excitation illumination to individual reaction regions or
groups of reaction regions, e.g. using waveguide arrays. When a
plurality, e.g., hundreds, thousands, millions or tens of millions,
of analyte regions are disposed upon a substrate, alignment of a
separate illumination beam with each analyte region becomes
technically more challenging and the risk of misalignment of the
beams and analyte regions increases. Alignment of the illumination
sources and analyte regions can be built into the system, however,
by integration of the illumination pattern and reaction regions
into the same component of the system, e.g., a target waveguide
device. In some cases, optical waveguides are fabricated into a
substrate at defined regions of the substrate, and analyte regions
are disposed upon the area(s) of the device occupied by the
waveguides.
Finally, in some aspects, substrates used in the target waveguide
devices are provided from rugged materials, e.g., silicon, glass,
quartz or polymeric or inorganic materials that have demonstrated
longevity in harsh environments, e.g., extremes of cold, heat,
chemical compositions, e.g., high salt, acidic or basic
environments, vacuum, and zero gravity. As such, they provide
rugged capabilities for a wide range of applications.
Waveguide devices used in the analytical systems of the present
specification generally include a matrix, e.g., a silica-based
matrix, such as silicon, glass, quartz or the like, polymeric
matrix, ceramic matrix, or other solid organic or inorganic
material conventionally employed in the fabrication of waveguide
substrates, and one or more waveguides disposed upon or within the
matrix, where the waveguides are configured to be optically coupled
through free space to an optical energy source, e.g., a laser,
optionally through an intervening optical fiber, a PLC, one or more
lenses, prisms, mirrors, or the like. Waveguides of the instant
integrated devices can be in various conformations, including but
not limited to planar waveguides and channel waveguides. Some
preferred embodiments of the waveguides comprise an array of two or
more waveguides, e.g., discrete channel waveguides, and such
waveguides are also referred to herein as waveguide arrays.
Further, channel waveguides can have different cross-sectional
dimensions and shapes, e.g., rectangular, circular, oval, lobed,
and the like; and in certain embodiments, different conformations
of waveguides, e.g., channel and/or planar, can be present in a
single waveguide device.
In typical embodiments, a waveguide in a target waveguide device
comprises an optical core and a waveguide cladding adjacent to the
optical core, where the optical core has a refractive index
sufficiently higher than the refractive index of the waveguide
cladding to promote containment and propagation of optical energy
through the core. In general, the waveguide cladding refers to a
portion of the substrate that is adjacent to and partially,
substantially, or completely surrounds the optical core. The
waveguide cladding layer can extend throughout the matrix, or the
matrix can comprise further "non-cladding" layers. A
"substrate-enclosed" waveguide or region thereof is entirely
surrounded by a non-cladding layer of matrix; a "surface-exposed"
waveguide or region thereof has at least a portion of the waveguide
cladding exposed on a surface of the substrate; and a
"core-exposed" waveguide or region thereof has at least a portion
of the core exposed on a surface of the substrate. Further, a
waveguide array can comprise discrete waveguides in various
conformations, including but not limited to, parallel,
perpendicular, convergent, divergent, entirely separate, branched,
end-joined, serpentine, and combinations thereof. In general, a
waveguide that is "disposed on" a substrate in one of the instant
devices, for example, a target waveguide device, can include any of
the above configurations or combinations thereof.
A surface or surface region of a waveguide device is generally a
portion of the device in contact with the space surrounding the
device, and such space can be fluid-filled, e.g., an analytical
reaction mixture containing various reaction components. In certain
preferred embodiments, substrate surfaces are provided in apertures
that descend into the substrate, and optionally into the waveguide
cladding and/or the optical core. As discussed above, in certain
specific embodiments, such apertures are very small, e.g., having
dimensions on the micrometer or nanometer scale.
The waveguides of the subject target devices provide illumination
via an evanescent field produced by the escape of optical energy
from the optical core. The evanescent field is the optical energy
field that decays exponentially as a function of distance from the
waveguide surface when optical energy passes through the waveguide.
As such, in order for an analyte of interest to be illuminated by
the waveguide, it must be disposed near enough to the optical core
to be exposed to the evanescent field. In preferred embodiments,
such analytes are immobilized, directly or indirectly, on a surface
of the target waveguide device. For example, immobilization can
take place on a surface-exposed waveguide, or within a nanowell
etched in the surface of the device. In some preferred aspects, the
nanowells extend through the device to bring the analyte regions
closer to the optical core. Such nanowells can extend through a
waveguide cladding surrounding the optical core, or can extend into
the core of the waveguide itself. Examples of using optical
waveguides to illuminate analytical samples in nanoscale reaction
volumes are provided in U.S. Pat. No. 7,820,983 and U.S. Patent
Application Publication No. 2012/0085894, which are incorporated by
reference herein in their entirety.
Target Waveguide Devices with Low Numerical Aperture
Because the target waveguide devices of the instant disclosure are
designed to be removable from an optical analytical system, and
because the tolerances between an optical source and its associated
target waveguide device must therefore be relatively relaxed, the
optical input, or inputs, of the instant integrated target
waveguide devices are configured to receive an optical signal, or
signals, through free space from an optical source. In particular,
the optical couplers of the instant target devices are configured
for coupling from the optical source through free space at a
distance of at least 1 mm, at least 2 mm, at least 3 mm, at least 5
mm, at least 10 mm, at least 20 mm, at least 30 mm, at least 50 mm,
at least 100 mm, or even longer distances. In some embodiments, the
devices are configured for optical coupling from the optical source
through free space at a distance of at least 5 mm. More
specifically, the coupling can be at a distance of at least 10 mm.
Even more specifically, the coupling can be at a distance of at
least 20 mm.
The instant devices can be configured to receive optical energy
through free space in a variety of ways. In particular, the
dimensions, shape, orientation, composition, and other properties
of the optical components of the devices are chosen to provide such
optical coupling through free space, as described in more detail
below and in the Examples section. In some embodiments, the optical
couplers of the target device are diffractive grating couplers,
although other optical couplers, such as endfire couplings, prism
couplings, or any other suitable optical input, can be usefully
coupled to the integrated waveguides in the instant devices.
Furthermore, the instant target waveguide devices preferably have
multiple optical inputs, so that the optical energy is coupled into
multiple independent waveguide pathways arrayed within the
device.
These and other features distinguish the instant devices and
systems from those typically used for optical transmission and
coupling in telecommunications and other related applications,
where optical sources are typically coupled to their targets
through extremely short distances. Indeed, the distances typically
coupled in an integrated telecommunications optical device are on
the order of 10 .mu.m or even less. For example, U.S. Patent
Application Publication No. 2014/0177995 discloses devices for
optical coupling from an integrated device to an external optical
fiber, where the outputs include couplers that comprise an
integrated waveguide structure, a mirror structure, and a tapered
vertical waveguide, where the vertical waveguide has apertures in
the range of 0.1 to 10 .mu.m and typical heights of 5-30 .mu.m.
These couplers, also known as vertical spot size converters, are
designed for direct or nearly direct connection between the
integrated waveguide structure and an associated output fiber. The
devices optionally include a microlens of diameter less than 1 mm
fabricated within the vertical waveguide. Another example of the
direct, or nearly direct, coupling between an integrated waveguide
device and an associated target optical fiber is provided in U.S.
Patent Application Publication No. 2015/0001175, which discloses
the use of cylinder-shaped or sphere-shaped microlenses to
facilitate optical coupling. The lenses are fabricated with radii
roughly the same as the .about.10 .mu.m mode size of a typical
telecommunications optical fiber, where the fiber is directly
abutted with the microlens. These couplers are thus also designed
for direct or nearly direct connection between the integrated
waveguide structure and the target fiber at the time of device
manufacture.
The target devices of the instant disclosure thus comprise an
optical coupler and an integrated waveguide that is optically
coupled to the optical coupler. In some embodiments, the optical
coupler of the instant devices is a low numerical aperture coupler,
and in some embodiments, the optical coupler is a diffraction
grating coupler.
Grating couplers and their use in coupling light, typically light
from optical fibers, to waveguide devices are known in the art. For
example, U.S. Pat. No. 3,674,335 discloses reflection and
transmission grating couplers suitable for routing light into a
thin film waveguide. In addition, U.S. Pat. No. 7,245,803 discloses
improved grating couplers comprising a plurality of elongate
scattering elements. The couplers preferably have a flared
structure with a narrow end and a wide end. The structures are said
to provide enhanced efficiency in coupling optical signals in and
out of planar waveguide structures. U.S. Pat. No. 7,194,166
discloses waveguide grating couplers suitable for coupling
wavelength division multiplexed light to and from single mode and
multimode optical fibers. The disclosed devices include a group of
waveguide grating couplers disposed on a surface that are all
illuminated by a spot of light from the fiber. At least one grating
coupler within the group of couplers is tuned to each channel in
the light beam, and the group of couplers thus demultiplexes the
channels propagating in the fiber. Additional examples of grating
couplers are disclosed in U.S. Pat. No. 7,792,402 and PCT
International Publication Nos. WO 2011/126718 and WO 2013/037900. A
combination of prism coupling and grating coupling of a
multi-wavelength optical source into an integrated waveguide device
is disclosed in U.S. Pat. No. 7,058,261.
FIGS. 1A-1C provide a general comparison between target waveguide
devices that are coupled directly, or nearly directly, to an
optical source with a high numerical aperture, and those, as
disclosed herein, where coupling is through free space to an
optical source with a low numerical aperture. As shown in FIG. 1A,
where light is coupled from an optical fiber (100) or other optical
source with high numerical aperture to a target waveguide device
(110), the optical beam (102) travels a relatively short distance
and thus displays a relatively small beam radius. As shown, the
optical beam illuminates a grating coupler (106) that is optically
connected to an integrated waveguide (108) within the target
device. For comparison, as shown in FIG. 1B, the target waveguide
devices of the instant disclosure (e.g., 160) are illuminated by an
optical beam (152) that travels a longer distance from the optical
source (150) and displays a larger beam radius than the system
shown in FIG. 1A. The larger beam, after optionally passing through
a lens element (154) or the like, illuminates a relatively larger
grating coupler (156) and is then launched into the optically
coupled integrated waveguide (158) associated with the coupler.
FIG. 1C illustrates an alternative embodiment of this type of
optical system. Specifically, in this system, one or more optical
elements (e.g., 184) are positioned between an optical source
(e.g., 180) and a target waveguide device (e.g., 190). Such optical
elements can serve to focus, collimate, or otherwise modify an
optical beam (e.g., 182) before it illuminates the target waveguide
device. The optical element can, for example, modulate the focus of
the beam to more closely match the numerical aperture (NA) of the
grating coupler (e.g., 186) on the target device, as would be
understood by those of ordinary skill in the art. The optical
element can likewise, for example, modulate the size of the
footprint of the beam on the grating coupler, as desired. As should
be understood from this example, the NA of the optical output of
the optical source need not exactly match the NA of the input
coupler on the target device, since an intervening lens or other
optical element can be used to modulate the optical properties of
the beam between the optical source and the target waveguide
device.
In one aspect, the instant disclosure therefore provides target
waveguide devices with one or more optical inputs that are
configured to couple light through free space from an optical
source or sources. The optical source can be delivered to the
target device through an intermediate optical component, for
example through a PLC or the like, such as the PLCs disclosed in
co-owned U.S. Patent Application No. 62/133,965 and Ser. No.
15/072,146. According to some embodiments, the numerical aperture
(NA) of the optical inputs in the target waveguide devices is
modulated in order to facilitate and optimize coupling into the
target device in various ways. As is understood by those of
ordinary skill in the optical arts, NA is related to the range of
angles within which light, in particular a light source
approximating a Gaussian light beam, can be accepted or emitted
from a lens, a fiber, a waveguide, a grating coupler, or the like.
It is a dimensionless value that, in the case of a Gaussian beam
impinging on an objective lens, can be calculated using the
following equation: NA=n sin .theta..sub.max where n is the index
of refraction of the medium through which the beam is propagated
and .theta..sub.max is the maximum acceptance angle of the lens.
This angle corresponds to the half-angle of the lens's acceptance
cone, i.e., the cone of light capable of entering or exiting the
lens.
In the case of a multi-mode optical fiber, the numerical aperture
depends on n.sub.core, the refractive index of the core, and
n.sub.clad, the refractive index of the cladding, according to the
following equation: NA= {square root over
(n.sub.core.sup.2-n.sub.clad.sup.2)} The NA of an optical device,
such as a fiber or an integrated waveguide, thus can depend on the
optical properties of the materials used to fabricate the device
(e.g., the core and the cladding of a fiber or waveguide) and the
size and geometry of the device. The NA also depends on the
wavelength of light being propagated through the device. It should
thus be understood that the NA of a particular optical device can
be usefully modulated to obtain suitable behavior of the device for
a particular application and purpose.
From a practical standpoint, the NA of a given optical device can
also be determined empirically, for example by measuring the
characteristics of propagated light emitted by the device at a
certain distance from the end of the device, for example using a
direct far field scanner according to specification EIA/TIA-455-47.
Such measurements provide empirical values of the mode field
diameter (MFD), effective area, and numerical aperture of the
optical device. In the case of a single-mode fiber, the MFD is
related to the spot size of the fundamental mode and represents a
far-field power distribution of the optical output of the fiber.
The relationship between NA and MFD for a Gaussian beam is provided
by the following equation, where .lamda. is the wavelength of
propagated light:
.pi..times..lamda. ##EQU00001##
Table 1 shows the relationship between NA and beam diameter for
light of 532 nm, where the Gaussian beam profile is truncated at
three different power levels: 1/e.sup.2, 1/e.sup.3, and 1/e.sup.4.
The listed beam diameters at a power truncation of 1/e.sup.2
correspond to the MFD of the beam for each value of NA. The listed
beam diameters at a power truncation of 1/e.sup.3 provide a useful
estimation in designing the size of an optical coupler on a target
device. More specifically, a coupler of the cross-sectional size
shown in this column will capture most of the energy from the
transmitted beam.
As is known in the art, single mode fiber devices are commonly used
in a variety of optical devices for the transmission and coupling
of optical signals, particularly in the telecommunications
industry. Such devices typically display NA values of 0.12 or
greater. As shown in Table 1, such NAs, for example NAs of 0.12 and
0.13, result in relatively narrow beam sizes at this wavelength of
light: 2.82 .mu.m and 2.61 .mu.m, respectively. By comparison, a
Gaussian beam of 532 nm light with an NA of 0.01 displays a beam
size of approximately 34 .mu.m--over 10 times larger. FIG. 2A shows
the 2-dimensional profile of such a Gaussian beam (NA equal to
0.01). As just noted, the beam size is determined by the truncation
of beam profile at the 1/e.sup.2 power level.
TABLE-US-00001 TABLE 1 Power-truncated beam profiles for light of
532 nm as a function of NA. 1/e.sup.2 1/e.sup.3 1/e.sup.4 NA
(.mu.m) (.mu.m) (.mu.m) 0.13 2.61 3.91 5.21 0.12 2.82 4.23 5.64
0.05 6.77 10.16 13.55 0.015 22.58 33.87 45.16 0.01 33.87 50.80
67.74 0.005 67.74 101.60 135.47
It should also be understood that the diameter of a Gaussian beam
will vary along the beam axis due to beam divergence. More
specifically, for a divergent Gaussian beam propagated in free
space, the beam radius, w, varies as a function of distance, z,
along the length of the beam axis according to the equation:
.function..times. ##EQU00002## where w.sub.0 is the minimum beam
radius, i.e., the "waist radius", that occurs at a particular
location along the beam axis known as the "beam waist", z is the
distance from the beam waist along the beam axis, and Z.sub.R is
the Rayleigh length, a constant for a given beam that depends on
the waist radius and the wavelength of light, .lamda., according
to:
.pi..times..times..lamda. ##EQU00003## Accordingly, at a distance
along the beam axis of z.sub.R from the beam waist, the beam radius
is equal to w.sub.0 {square root over (2)}. In view of the above,
it also follows that the Rayleigh length and the numerical aperture
are related to one another according to the following equation:
##EQU00004## The above parameters are illustrated graphically in
FIG. 2B, which represents a divergent Gaussian beam of radius
w.
In accordance with the above description, lenses, fibers, and
waveguides with relatively large NA values are typically used to
illuminate target surfaces over short distances through free space,
and the spot size of such illumination is typically small. These
distinctions are apparent in the exemplary systems illustrated
graphically in FIGS. 1A and 1B. Specifically, the optical device
(100) of the system shown in FIG. 1A (e.g., an optical fiber) has a
high NA, and is best suited for illuminating a small-diameter
coupler at close proximity to the target waveguide device (110). By
comparison, the optical source (150) and lens (154) of the system
shown in FIG. 1B has a low NA, and, as described herein, is well
suited for illuminating a large-diameter coupler at a large
free-space coupling distance. As mentioned above, FIG. 1C shows an
alternative design that permits the optical footprint of the output
beam to be re-imaged with a target magnification, for example using
an intervening optical element, to provide a beam waist of a
preferred size at the surface of the target device. It should be
further noted here that the illustrations provided throughout the
disclosure are not necessarily intended to represent accurately the
dimensions, angles, or other specific design features of the
devices illustrated, in particular any representation of divergence
angles, beam radii, layer thicknesses, waveguide bend radii,
specific routing paths, and so forth.
Free-space coupling, as disclosed in the devices and systems
herein, provides several advantages relative to the direct, or
nearly direct, coupling typically used in telecommunications and
related systems. First, coupling through free space avoids
near-surface fiber tip to chip operation and is thus much easier
for installation and operation and much less vulnerable to
chip-surface dust and contamination and tip damage due to
mis-operation of optical analytical systems with removable target
waveguide devices. Second, as illustrated in FIGS. 1B and 1C,
coupling with low NA delivery devices through free space allows
larger beam diameters on the target waveguide device, thus
relieving thermal constraints on the target chip due to the
injection of high laser power. Third, larger grating coupler size
also greatly alleviates optical source-to-chip alignment
difficulties and minimizes the impact of dust and other
contaminants on the coupler surface. Fourth, free-space coupling
allows easier chip packaging solutions for the target chip, which,
for example in a multiplexed DNA sequencing chip, needs to
accommodate all the packaging interface requirements such as
electrical, thermal, mechanical, and fluidics components. Use of
larger couplers is particularly advantageous in applications where
surface-area constraints are not of overriding importance, for
example in some applications using commercial CMOS chips. In view
of the above, it should be apparent that the input NA of the
instant target waveguide devices can thus be modulated in order to
improve and optimize optical coupling from an associated optical
source.
Accordingly, the instant disclosure provides target waveguide
devices with one or more optical inputs that are configured to
couple light through free space from an optical source or sources
through a high-efficiency input coupler. Such devices can
optionally comprise additional features, for example further
integrated waveguides, preferably in an array, and a plurality of
nanowells optically coupled to the waveguide or array of
waveguides. As described above, an array of nanowells in optical
connection with an excitation source can be usefully employed, for
example, in the performance of highly-multiplexed DNA sequencing
reactions using fluorescently-labeled nucleotide reagents.
The free-space coupling of optical energy into the instant target
devices is preferably achieved through the use of a
high-efficiency, low-NA grating coupler. An exemplary grating
coupler is illustrated in FIG. 3A. Such couplers are conveniently
prepared using standard semiconductor processing techniques on, for
example, a silicon chip or other suitable substrate (320). The
grating typically includes a bottom cladding layer (324), a
waveguide core layer (308), and a top cladding layer (322), where
the core layer has a higher refractive index than the cladding
layers, so that light injected into the core is propagated by total
internal reflection at the core/cladding boundaries. A grating
structure (306) is created in the waveguide core, typically during
the fabrication process, with a desired duty cycle (312), etch
depth (314), and grating period (316), such that optical energy
(302) incident on the surface of the grating can enter the grating
and be efficiently propagated down the waveguide core. FIG. 3B
shows a variant of the grating coupler of FIG. 3A, where the
waveguide core is etched as shown to provide a "blazed" coupler
region (326).
The detailed grating coupler structures and shapes can be varied in
a number of ways to improve the coupling efficiency. For a simple
binary grating coupler, the structure can be etched from the top
only, as illustrated in FIGS. 3A, 3B, and 3E, or from the bottom
only, as illustrated in FIG. 3C. Alternatively, the structure can
be double-sided etched from both the top and the bottom, as
illustrated in FIGS. 3D and 3F. Moreover, an overlay layer can be
added to the structure to the increase the teeth height, as
illustrated in the grating coupler structures of FIGS. 3E and 3F,
thus further improving the coupling efficiencies of the gratings.
The period of the grating coupler can be fixed as a uniform
grating, or it can be "chirped" with a certain function, by
fabricating the teeth with a non-uniform period, to better match
the Gaussian beam profile, as illustrated in the grating coupler
(346) illustrated in FIG. 3G, thus improving the coupling
efficiency. Alternatively, or in addition, a bottom reflective
layer (370) can be added to the structure, as illustrated in FIG.
3H, to reflect the down-coupling light and thus to improve coupling
efficiency.
In some embodiments, the grating period of the instant grating
couplers is in the range from 300 nm to 1000 nm. In more specific
embodiments, the grating period is in the range from 300 nm to 500
nm and from 300 nm to 400 nm. In even more specific embodiments,
the grating period is from 340 nm to 380 nm and can in some
embodiments be approximately 355 nm. In other even more specific
embodiments, the grating period is from 300 nm to 340 nm and can in
some embodiments be approximately 315 nm.
In some embodiments, the etch width of the instant grating couplers
is in the range from 150 nm to 500 nm. In more specific
embodiments, the etch width is in the range from 150 nm to 400 nm.
In even more specific embodiments, the etch width is in the range
from 150 to 300 nm and can in some embodiments be approximately 185
nm.
In embodiments, the etch depth of the instant grating couplers is
in the range from 30 nm to 200 nm, is in the range from 50 nm to
150 nm, or is in the range from 50 nm to 100 nm. Specifically, the
etch depth can be approximately 68 nm. In some embodiments, the
etch depth is in the range from 30 nm to 80 nm. Specifically, the
etch depth can be approximately 55 nm.
The thickness of the waveguide core of the instant grating couplers
is preferably optimized for single-mode operation using light of a
desired wavelength. The optimal core thickness ("d") can
accordingly be estimated using the following relationship:
.pi..times..times..lamda..times.<.pi.<.lamda. ##EQU00005##
For a typical waveguide construction, with a silicon nitride core
(e.g., n.sub.core.apprxeq.1.9085) and a silicon dioxide cladding
(e.g., n.sub.clad.apprxeq.1.46), a core thickness of about 217 nm
is optimal for light with wavelength of 532 nm, and a core
thickness of about 225 nm is optimal for light with wavelength of
552 nm. Where the refractive index of the waveguide core is
increased, for example by using a titanium oxide core, or the like,
optimal core thicknesses can be significantly smaller. For example,
where n.sub.core=2.55 and n.sub.clad=1.46, optimal core thicknesses
of 127 nm (@532 nm) and 132 nm (@552 nm) can be estimated. In view
of the above, the waveguide core thickness of the instant grating
couplers can range from about 100 nm to about 300 nm. More
specifically, the waveguide core thickness can range from about 100
nm to about 150 nm, and even more specifically from about 125 nm to
about 135 nm. In some embodiments, the waveguide core thickness can
range from about 150 nm to about 250 nm, more specifically from
about 200 nm to about 240 nm, and even more specifically from about
215 nm to about 230 nm. In some embodiments, the waveguide core
thickness can be approximately 180 nm.
In embodiments, the waveguide core refractive index of the instant
grating couplers is in the range from 1.9 to 3.5 and more
specifically is approximately 1.9. In some embodiments, the
waveguide core refractive index is in the range from about 2.4 to
about 2.7, more specifically from about 2.5 to about 2.6. In
embodiments, the top cladding thickness of the instant grating
couplers is in the range from 250 nm to 1000 nm, more specifically
is approximately 280 nm. In embodiments, the bottom cladding
thickness of the instant grating couplers is in the range from 2
.mu.m to 10 .mu.m and more specifically is approximately 2.1 .mu.m.
In embodiments, the cladding refractive index of the instant
grating couplers is in the range from 1 to 2 and is more
specifically approximately 1.47. It should be understood that
refractive indices are preferably specified for a given material at
the wavelength of light being transmitted through the material, as
would be understood by those of ordinary skill in the art.
In device embodiments comprising a reflective layer, the reflector
distance (from coupler bottom to the reflector) of the devices can
be in the range from 250 nm to 500 nm and can be more specifically
approximately 260 nm.
As mentioned above, the NA of the instant target waveguide devices
can be modulated in order to improve coupling from the optical
source through free space. In embodiments, the NA of the target
waveguide device is modulated to match the NA of the optical
source. According to some embodiments, the optical input of the
instant devices has a numerical aperture of no more than 0.1, no
more than 0.08, no more than 0.05, no more than 0.03, no more than
0.02, no more than 0.01, no more than 0.005, or even lower. In some
embodiments, the numerical aperture is no more than 0.05. In
specific embodiments, the numerical aperture is no more than
0.015.
As should be apparent from the comparison shown in FIGS. 1A and 1B,
although the NA of traditional optical sources and targets (e.g.,
100 and 110) is significantly higher than that of the optical
sources and targets used in the instant systems (e.g., 150 and
160), the surface area or "footprint" illuminated on the instant
target devices is larger. (For example, compare the size of grating
couplers 106 and 156.) As noted above, larger optical footprints
can be advantageous inter alia in minimizing heating of the target
device and/or in simplifying alignment of the optical source and
the target device. In particular, the power intensity of the
transmitted light is much lower than it would be if the light were
transmitted in a more focused beam.
The exact spot size of light delivered to a target waveguide device
will, of course, depend both on the NA of the optical outputs of
the optical source and the free space distance between the optical
source and the target device. In embodiments, the target waveguide
device is designed with a coupler size that matches the spot size
of illumination from the optical source. In embodiments, the
coupler size of the target device is at least 100 .mu.m.sup.2, at
least 144 .mu.m.sup.2, at least 225 .mu.m.sup.2, at least 400
.mu.m.sup.2, at least 625 .mu.m.sup.2, at least 900 .mu.m.sup.2, at
least 1600 .mu.m.sup.2, at least 2500 .mu.m.sup.2, at least 4900
.mu.m.sup.2, at least 10,000 .mu.m.sup.2, or even larger.
In other embodiments, the coupler size of the target device is at
most 250,000 .mu.m.sup.2, at most 62,500 .mu.m.sup.2, at most
22,500 .mu.m.sup.2, at most 10,000 .mu.m.sup.2, at most 6400
.mu.m.sup.2, at most 3600 .mu.m.sup.2, or at most 2500
.mu.m.sup.2.
In specific embodiments, the coupler size of the target device is
from 100 .mu.m.sup.2 to 250,000 .mu.m.sup.2, from 225 .mu.m.sup.2
to 62,500 .mu.m.sup.2, from 400 .mu.m.sup.2 to 22,500 .mu.m.sup.2,
from 625 .mu.m.sup.2 to 10,000 .mu.m.sup.2, from 900 .mu.m.sup.2 to
6400 .mu.m.sup.2, or from 1600 .mu.m.sup.2 to 3600 .mu.m.sup.2.
In embodiments, the above-described illuminations are achieved at a
free-space distance between the optical source and the target
device of from 1 mm to 100 mm. More specifically, the free-space
distance can be from 2 mm to 90 mm, from 5 mm to 80 mm, from 10 mm
to 60 mm, or even from 20 mm to 50 mm.
It also follows from the above description that the instant target
waveguide devices are capable of receiving relatively high levels
of optical energy from an optical source due to the relatively
large spot sizes illuminated on the target device. Accordingly, in
embodiments, the target device is configured to receive optical
energy with power per coupler of at least 1 mW, at least 2 mW, at
least 3 mW, at least 5 mW, at least 10 mW, at least 20 mW, at least
30 mW, at least 50 mW, at least 100 mW, or even higher per coupler.
In specific embodiments, these power levels are achieved at a
free-space distance of at least 10 mm.
According to another aspect of the disclosure, it can be desirable
to modulate the design of the integrated waveguides in the target
waveguide device in order to improve the coupling between the
optical source and the target waveguide device. In particular, it
can be desirable to modulate the composition and shape of the
integrated waveguides to achieve these effects. For example, it is
known in the field of optics that mismatches between the mode sizes
and effective indices between the highly confined mode of an
integrated optical waveguide and the large diameter mode of an
optical fiber input can result in coupling losses if not addressed.
It can therefore be advantageous to taper the waveguide geometry or
otherwise vary the waveguide structure and/or composition in order
to improve the behavior and efficiency of the device, particularly
in transitions between confined and unconfined optical modes. Such
variation in structure and composition can include, for example,
modulation of cladding composition and geometry or modulation of
core composition and geometry. In particular, core cross-sectional
geometry can be modulated to improve coupling efficiencies. These
and other features can be modeled and tested using widely available
commercial software to predict and optimize the photonic properties
of the devices prior to their fabrication.
In some applications, it can be advantageous to vary the optical
power emitted from each optical output of an optical source
according to the specific requirements of the target device, for
example to compensate for propagation losses as the light passes
through the target waveguides. Such approaches are described in
co-owned U.S. Patent Application No. 62/133,965 and Ser. No.
15/072,146. Other advantageous features and designs that can
optionally be included in the instant target waveguide devices are
disclosed in U.S. Patent Application Publication Nos. 2014/0199016
and 2014/0287964, which are incorporated by reference herein in
their entireties.
The waveguide devices and systems of the instant disclosure can be
further distinguished from those typically used in transmitting
optical signals in telecommunications applications. In particular,
the instant target waveguide devices are designed for use with
higher intensity optical energy, and they are designed to transmit
that energy for much shorter distances. In addition, the
wavelengths of light transmitted by these devices are suitable for
use with the optically active reagents commonly used in biological
assays. These wavelengths are generally significantly shorter than
those used for telecommunications purposes. In particular, the
optical illumination used in DNA sequencing reactions with
fluorescently-labeled DNA reagents, is typically in the visible
range, most commonly in the range from 450 nm to 650 nm. The
waveguides and other components of the target devices and systems
disclosed herein are therefore preferably designed and scaled to
transmit optical energy efficiently in the visible range. In some
embodiments, the wavelengths range from about 400 nm to about 700
nm. In more specific embodiments, the wavelengths range from about
450 nm to 650 nm or even from about 500 nm to about 600 nm. In some
specific embodiments, the wavelengths are from about 520 nm to
about 540 nm, for example, approximately 532 nm. In other specific
embodiments, the wavelengths are from about 620 nm to about 660 nm,
for example, approximately 635 nm or 650 nm. In still other
specific embodiments, the devices are designed for optimal
transmission of light having wavelengths from about 540 nm to about
560 nm, for example, approximately 552 nm. In some embodiments,
multiple wavelengths of visible light can be transmitted within the
devices simultaneously. A silicon nitride waveguide device,
including an integrated grating coupler, for the transmission of
visible wavelengths has recently been reported. Romero-Garcia et
al. (2013) Opt. Express 21, 14036. Accordingly, in some
embodiments, the waveguide core material is a silicon nitride. In
other embodiments, the waveguide core material is a material having
an even higher refractive index at the wavelengths used in the
instant device, for example a titanium oxide, such as titanium
dioxide (TiO.sub.2). Such higher refractive index materials also
preferably display low autofluorescence.
The grating couplers of the instant devices may in some embodiments
be beam focusing couplers. In particular, in order to avoid the
long taper associated with the reduction of mode size from the
large footprint, low-NA grating couplers (where mode size can be,
for example, 50 .mu.m) to a mode size effective in illuminating
nanoscale sample wells (for example, 0.5 .mu.m), the shape of the
coupler can be changed from rectangular (as viewed from the top) to
tapered (as viewed from the top) to form an ultracompact focusing
grating coupler. The top view of one such exemplary coupler design
is illustrated in FIG. 3I.
Beam focusing couplers may bend the grating lines to be a series of
confocal ellipses with the focal point located at the
grating-waveguide interface. Therefore, the optical mode can be
directly focused from the grating to the waveguide in a much
smaller distance, in some cases on the order of several hundred
microns. As illustrated in FIGS. 3J and 3K, which are also top
views of the couplers, the transition region between the grating
coupler and the integrated waveguide core can, for example, be a
tapered waveguide (FIG. 3J) or a slab waveguide (FIG. 3K). In each
case, the curved grating lines focus the light into the aperture of
the integrated waveguide. Also identified in these figures are two
relevant parameters--focal length and defocus--that are of
importance in the design of a beam focusing coupler. Furthermore,
as shown with the slab waveguide transition region of FIG. 3K, the
aperture of the integrated waveguide targeted by the grating
coupler can be tapered to a wider width in order to achieve optimal
coupling. FIG. 3L illustrates a cross-sectional profile of an
exemplary focusing grating coupler, indicating preferred chemical
compositions of the various layers and exemplary dimensions of the
various features.
In this regard, for some target waveguide device embodiments, where
the coupler is a focusing grating coupler, the focusing coupler
focal length can be in the range from 150 .mu.m to 500 .mu.m and
can be more specifically approximately 170 .mu.m. In some
embodiments, the focusing coupler defocus of the instant grating
couplers is in the range from 0 to 10 .mu.m and is more
specifically approximately 0 .mu.m. In some embodiments, the
focusing coupler aperture width is in the range from 1 .mu.m to 5
.mu.m and is more specifically approximately 3 .mu.m. In some
embodiments, the waveguide taper length of the focusing grating
couplers is in the range from 50 .mu.m to 200 .mu.m and is more
specifically approximately 75 .mu.m. In some embodiments, the
coupling angle of the instant grating couplers is in the range of
10 degrees+/-2 degrees. In a specific design, the coupler is a slab
coupler with focal length=150 .mu.m, defocus=0, and aperture
width=3 .mu.m.
Furthermore, the above design features and parameters of a target
waveguide device can be combined, in any suitable way, to maximize
the coupling efficiency. The design and fabrication of the
above-described structures is within the skill of those of ordinary
skill in the art. Exemplary grating couplers are described in the
references provided above. Other exemplary waveguide devices with
grating couplers, including focusing couplers and couplers with
reflective metallic layers, have also been reported. See, e.g.,
Waldhausl et al. (1997) Applied Optics 36, 9383; van Laere et al.
(2007) J. Lightwave Technol. 25, 151; van Laere et al. (2007) DOI:
10.1109/OFC.2007.4348869 (Optical Fiber Communication and the
National Fiber Optic Engineers Conference); U.S. Pat. No.
7,283,705. It should be understood, however, that the couplers
disclosed in these references are typically designed for optimal
coupling from high-NA optical sources, not from low-NA optical
sources.
Target Waveguide Devices with Alignment Features
In some embodiments, the target devices and systems of the instant
disclosure include features that provide free-space coupling
between an optical source and a target device while maintaining
alignment of the components to sub-micron accuracy in space,
including angle tolerances. Disturbances communicated to the
analytical system from the mounting such as shocks and vibrations
may cause alignment errors that are substantial on the submicron
scale. Pneumatic isolation, which has been used in some prior art
analytical systems, is physically large, and expensive, in order to
reject these perturbations passively. An alternative to such
passive approaches is the use of an active rejection by estimation
of an alignment error, and commanding a correction, and possibly
iterating depending on the particular response of the physical
servo system. This active rejection of vibration can be small,
inexpensive, and highly effective: however, this active rejection
requires an error signal. On the time scales of interest, the image
correlation approaches used in some prior art instruments to
estimate an error are insufficiently fast. Hill climbing based on a
dither (or perturb and observe) require higher bandwidth, more
expensive actuators, or are insufficiently fast.
The dynamic alignment approach disclosed herein involves one or
more alignment features that can be inexpensively incorporated into
a target waveguide device within an optical analytical system. Such
alignment features are used in combination with an alignment
detector, such as an alignment camera, within the analytical system
to provide a continuous estimate of alignment error, thus enabling
an inexpensive actuation and detection system.
In some embodiments, the alignment features take the form of
additional grating couplers, which may or may not be the same
design as the grating couplers used to couple the main pump power
into the device. The grating couplers couple input optical signals
into associated alignment waveguides. They can be arranged in at
least one, often 2, and sometimes more locations to better estimate
magnification, roll, and other errors. The alignment structures
detect the light from one or more alignment or "outrigger" light
beams that are directed toward the target waveguide. The alignment
light beams typically emanate from the same optical source as the
one or more sample excitation light beams (i.e., the light beams
targeting the analytical samples), so that the position of the
alignment beams can be used as a proxy for the position of the one
or more sample excitation light beams.
The input couplers of the alignment waveguides direct coupled light
from designated beams to designated output couplers, which may or
may not be grating couplers. These output couplers should be
readily distinguishable from one another, so that the output power
can be uniquely estimated for each. For example, where a low NA
external camera is used as a detector, the spacing can be
.about.150 .mu.m.
The output estimated for each output device can then be combined,
typically with a simple formula, to form what is designated a
tracking error signal (TES). This TES, for each dimension of
interest, can then be converted into a command to counter the
present state of misalignment. An exemplary arrangement of
alignment couplers, together with their associated alignment
waveguides and output couplers, and sample excitation couplers,
together with their associated sample excitation or "sequencing"
waveguides, is shown in FIG. 4A. As shown, this exemplary target
waveguide device includes two triads of alignment waveguides, shown
as the top three coupler/waveguide combinations and the bottom
three coupler/waveguide combinations in the drawing. Each triad of
alignment couplers is illuminated by a single optical input,
illustrated as a circular shaded region in the drawing, so that the
portion of light passing through each of the waveguides depends on
the alignment of the optical input with each alignment coupler. The
output from the alignment waveguides, designated A1, B1, and C1 for
the top triad of alignment waveguides and A2, B2, and C2 for the
bottom triad of alignment waveguides, is monitored by a camera or
other suitable alignment detector device to generate a TES. If the
optical source and target device move relative to one another
during a measurement, it is apparent that the TES generated by each
trio of waveguides will change. Alignment can be maintained, and
misalignment can be reversed, by monitoring the TES values. Each
triad of alignment input and output couplers and their associated
alignment waveguides should be considered a single alignment
feature for purposes of this disclosure.
Also shown in the device of FIG. 4A are sample excitation couplers,
in this case fabricated between the two triads of alignment
couplers. The sample excitation couplers are used to deliver
optical energy from the input beams, which are identified in FIG.
4A as circular shaded regions within each coupler, to the
analytical nanoscale samples within the device, typically through a
fanout region of the device. The fanout region splits the incoming
excitation signal into a larger number of split waveguides for
delivery to the arrays of nanoscale sample wells in the device. One
or more of the sample excitation waveguides associated with each
input coupler can additionally be used to monitor power levels of
optical energy input into the sample excitation input coupler.
These power monitoring waveguides can deliver their optical signals
to an output coupler for monitoring by a power output detector. In
some embodiments, for example as shown in the device of FIG. 4A,
the power output monitoring couplers, identified as circular shaded
regions at the end of the "sequencing WGs" in FIG. 4A, are located
near the alignment waveguide output couplers. In these embodiments,
a single detector, for example a single camera, can be used to
monitor both the alignment waveguide signals and the sample
excitation waveguide power output monitoring signals
simultaneously.
The input couplers of the alignment waveguides and the input
coupler of a sample excitation waveguide (labeled as a "low NA
input coupler") are shown in closer detail in FIG. 4B. The optical
input for the alignment feature in this exemplary device is a 1%
beam, that is, the alignment beam carries about 1% of the power of
all of the combined beams reaching the device. The optical input
for the sample excitation coupler is a full-power beam, also known
as a "sequencing beam" or a "pump-power beam". The footprints
illuminated by these beams are illustrated as shaded circles in
FIG. 4A and as open circles in FIG. 4B. Approximate dimensions of
the exemplary input couplers are also shown in FIG. 4B.
Another exemplary arrangement of alignment features in a target
waveguide device is illustrated schematically in FIG. 4C. This
device includes two "patterned", or "stipled", regions (460) that
can serve as alignment features. These features can work
independently of, or in addition to, the alignment features
described above in FIGS. 4A and 4B and as also shown in the device
of FIG. 4C. The patterned regions on the device of FIG. 4C can be
illuminated by alignment beams, which are identified in the drawing
as shaded circles (470). As previously mentioned, the alignment
beams preferably carry approximately 1% of the power of the other
beams. The illuminated patterned regions can thus be observed and
monitored by a camera or other detector device within the
analytical device in order to establish and/or maintain alignment
of the optical source and the target waveguide. As just mentioned,
the target device of FIG. 4C also includes two of the
above-described alignment features, which comprise triads of
alignment input couplers (462), their associated alignment
waveguides (464), and their associated alignment output couplers
(466). The alignment output couplers are typically high numerical
aperture output couplers, which may be monitored from above by an
alignment detector, such as an alignment camera, to facilitate
alignment of the optical source and target waveguide device.
FIG. 4C also shows four shaded circles (472) representing the spots
illuminated by sample excitation beams from an optical source.
These full-power beams are coupled into the device through free
space, preferably using low numerical aperture couplers, as
described in detail elsewhere in the disclosure. As shown in the
drawing, in this embodiment of the target device, the couplers
direct the input optical energy from an optical source into tapered
integrated waveguides which are directed through "fanout" regions
to split the sample excitation beams into a larger number of split
sample excitation waveguides, in this case 10 split waveguides for
each input beam. The split waveguides ultimately deliver the input
optical energy to nanoscale sample wells arrayed on the device. In
the device of FIG. 4C, one of the 10 split waveguides associated
with each coupler is directed to an output coupler (474) to serve
as a power monitoring coupler, as described above. This coupler can
be observed by an external detector, such as a detector camera, to
monitor power levels passing through the excitation waveguides. The
power monitoring couplers can provide immediate feedback to the
system if the power output of an optical source changes during a
measurement, or if alignment is lost between the optical source and
the target waveguide device.
FIG. 4D illustrates another exemplary target waveguide device
(480). This device includes an input coupling region (481) in the
lower left corner of the device and a large arrayed nanoscale
sample well region (490) in the main central upper portion of the
device. The input coupling region can further include alignment
features, as described in detail above. FIG. 4D also illustrates
two sample excitation waveguide pathways, one starting at low NA
input coupler 482, and the other starting at low NA input coupler
484. Input sample excitation beams are coupled into these pathways
and directed to the nanoscale sample wells either through the top
fanout region (483) for input coupler 482 or through the bottom
fanout region (485) for input coupler 484. Within the fanout
regions, the excitation waveguides are split multiple times to
create an array of split excitation waveguides to deliver optical
energy to the nanoscale sample wells. As described in detail in
co-owned U.S. Patent Application No. 62/133,965 and Ser. No.
15/072,146, the different path lengths encountered by optical
energy that is input into the different couplers, and thus the
different propagation losses suffered by the different excitation
waveguide pathways, can be compensated by adjusting the power
levels of optical inputs from the different couplers or by
modulating the optical signals in other ways. The example of FIG.
4D also illustrates that the nanoscale samples can optionally be
excited by optical energy transported through the same excitation
waveguides from two different directions simultaneously. As shown
in this drawing, light delivered from input coupler 482 and light
delivered from input coupler 484 can be directed to the same
nanoscale sample wells through their associated arrayed waveguides
from opposite directions, if desired.
FIG. 4E illustrates an optical analytical system of the instant
disclosure, including a target waveguide device with at least one
of the alignment features described in this section. The system
comprises an optical source consisting of one or more lasers, a
beam power controller, and a "light brush", which may correspond to
one of the optical delivery devices of co-owned U.S. Patent
Application No. 62/133,965 and Ser. No. 15/072,146. The system also
comprises an alignment camera, an integrated detector component
comprising an array of "pixels" for detecting optical outputs from
nanoscale sample wells arrayed across the target device, and a
"sensor readout" component that receives and analyzes signals from
the detector. An optical beam or beams emitted by the lasers and
passing through the beam power controller and light brush is
represented as a thick arrow that illuminates an input coupler on
the target device. The optical input is coupled into the device and
is directed to one or more integrated waveguides within the device,
as indicated by the smaller arrow. The optical input can optionally
be directed to one or more alignment waveguides and/or one or more
power monitoring waveguides. The alignment camera in this drawing
is shown receiving optical outputs indicated in the drawing by even
smaller arrows, from output couplers at the far end of the device.
These couplers could be used to output light from the alignment
waveguides and/or the power monitoring waveguides. It should also
be understood that the alignment camera can, in addition or
alternatively, receive optical signals from other alignment
features such as one or more patterned regions, fiducials, or other
reference marks on the surface of the target device. Optical energy
traveling through the sample excitation waveguides illuminates
samples in the arrayed nanowells, and fluorescence emitted from the
samples is directed to appropriately aligned pixels in the detector
layer, where the output signal is measured.
FIG. 4F illustrates in graphic form how the light brush of FIG. 4E
can be aligned with the target waveguide device that is disclosed
herein, using any of the alignment features described above.
Specifically, this figure illustrates the degrees of freedom that
can be monitored and adjusted during the alignment of an optical
source and a target device. As shown in the drawing, the airplane
symbolizes three dimensions of rotation relative to the target
device, and the "cell surface" corresponds to the surface of the
target device. In addition to the rotational motions indicated in
the drawing as pitch, yaw, and roll (or pattern rotation), the
light brush and target device can move relative to one another in
the x, y, and z coordinate space. Two of these motions are shown in
the drawing as "along track" (AT) and "cross track" (CT) motions.
Not shown in the drawing is an up and down motion to vary the
distance between the light brush and target waveguide. As shown in
the inset drawing, rotation on the "roll" axis causes the input
beams to pivot around a particular axis. In this specific example,
the light brush provides 12 separate input "beamlets". The two
beamlets at each end of the illumination pattern are low-power
alignment beamlets. Their targets on the device are illustrated as
smaller circles in the line of input couplers on the surface of the
device.
Accordingly, as described above, the alignment features of the
instant disclosure can be arranged in various ways for various
purposes. For example, as described above, they can be arranged to
normalize for incident power. As also described above, the
alignment features can be used as pump power grating couplers, at
the expense of some efficiency. In addition, the output monitoring
devices can be grating couplers, or can be other devices that are
configured to redirect light towards an alignment detector, such as
a camera.
Furthermore, the light coupled into the alignment grating couplers
can be of the same wavelength as the pump power, but need not be.
Likewise polarization, input (and output) angles can differ from
the pump grating couplers, as desired. The light in the alignment
grating couplers can be either coherent or incoherent with the pump
grating couplers.
Accordingly, in some specific embodiments, the alignment feature
can comprise one or more waveguides. In more specific embodiments,
the alignment feature can comprise a plurality of low-power
waveguide taps or a high-power beam tap. In other embodiments, the
alignment feature can comprise a reference mark, for example a
fiducial or other type of patterned region. The use of reference
marks in the alignment of different components of an optical
analytical system is well known in the art of printed circuit board
manufacture and computer vision. See, for example, U.S. Pat. Nos.
5,140,646 and 7,831,098. The positional information obtained
through monitoring the alignment features of the instant devices by
an alignment detector can be used by the optical system to position
the optical source and the target device relative to one another
prior to the start of an analytical assay. The positional
information can further be used during the course of an assay to
maintain the position of the optical source and the target device
dynamically through a feedback loop, as would be understood by
those of skill in the art.
Target Waveguide Devices with Improved Power Handling
In some embodiments, the target waveguide devices of the instant
disclosure comprise grating couplers with improved power handling
capacity. In particular, one key factor limiting the amount of
optical power that can be coupled through a grating coupler is the
peak local temperature rise in the vicinity of a focused light beam
of high optical power density. With parameters reasonable for
optical coupling performance and typical materials and designs, the
local temperature in a region below the coupler can quickly reach
levels that are likely to impair performance or cause physical
damage, even with moderate input power (e.g., potentially much less
than 1 W).
Indeed, while various examples exist of grating couplers as an
interface between free-space or fiber optic inputs and waveguides
in microfabricated integrated photonic circuits, issues may arise
when such couplers are used to transmit substantial amounts of
optical power. While perfect coupling efficiency is unattainable,
and with the best reported coupling efficiencies in the range of
50% (i.e., -3 dB), a substantial fraction of incident power is not
coupled into the waveguide. Even if a substantial portion of the
uncoupled power is reflected or scattered away from the vicinity of
the coupler, however, some local absorption is inevitable. With
increasing input power, temperature in the vicinity of local
absorption for a tightly-focused beam may rise to levels that may
impair coupler performance or cause physical damage.
As described herein, however, by reducing the local thermal
resistance between a limited absorbing region and the bulk of the
microfabricated component, higher input power can be coupled
without damage or impairment of coupler performance. For a
fluorescence application, this means that greater pump intensity
can be utilized to improve signal-to-noise performance, and an
increased area or number of sample sites can be interrogated. In
addition, for the instant target devices and systems, where a
plurality of input ports can be required due to thermal
limitations, allowing more power per input port allows the number
of input ports to be reduced, thus simplifying the optical system
and the associated target device.
Accordingly, in the grating couplers of the instant target devices,
a layer of material with relatively high thermal conductivity can
be fabricated below the grating in order to improve the lateral
heat transfer within the device and thus reduce peak
temperatures.
If the design of the coupler includes a reflection layer below the
grating (optionally with some bottom cladding material in between)
in order to improve coupling efficiency, then the conductive layer
can be located immediately below and in contact with the layer of
material that forms the reflection layer interface with the bottom
cladding. Depending on materials, the interface between the
conductive layer and the bottom cladding below the coupler can
itself form the reflection layer, e.g., in the case of an interface
between SiO.sub.2 and Al for visible-wavelength applications.
In order to serve as an effective heat spreader, the
thermally-conductive layer should have a thickness greater than
required for purely optical purposes (which can in specific
embodiments be only on the order of 10 nm). In some embodiments,
the heat spreading layer can be from 10 nm to 1000 nm thick. In
more specific embodiments, the layer can be from 20 nm to 500 nm
thick. In even more specific embodiments, the layer can be from 50
to 250 nm thick. A dielectric stack can optionally be provided
above the conductive layer in order to further reduce absorption
and thus peak heat load.
In particular, in some embodiments, the operating wavelength,
numerical aperture/mode size, materials used for fabrication of the
grating coupler and specific design of the grating coupler (e.g.,
binary grating, blazed grating, focusing grating, etc.) can be
varied. In addition, the materials and process details for
fabrication of the heat spreader can be varied--e.g., any
sufficiently thermally conductive material that is appropriately
process-compatible could be used for the heat spreader. For
example, aluminum, tungsten, silicon carbide, copper, indium, tin,
titanium nitride, or others can be used depending on the process
technology. In specific embodiments, the thermally conductive
material is aluminum. Additional thin film layers can be provided
above the heat spreader in order to tailor optical performance
(e.g., reflection and absorption for a particular wavelength,
polarization, etc.).
The specific dimensions of the heat spreader (e.g., lateral extent
and thickness) can be varied to suit relevant design constraints,
including photonic circuit geometry, materials, and expected power.
While a reflective layer below a grating coupler can be made of a
material that has relatively high thermal conductivity and thus can
itself act as a heat spreader to some extent, the required
thickness of such a reflective layer from an optical perspective
can be quite small (e.g., 10-100 nm); at such thickness,
performance as a heat spreader is accordingly somewhat limited.
When the layer thickness is substantially greater than required for
optical purposes (e.g., 100 nm to 1 .mu.m or more, depending on the
geometry and materials used) heat spreading performance can be
substantially improved.
Exemplary target waveguide structures are illustrated graphically
in FIG. 5, where the structures of FIGS. 5A and 5B do not include
heat spreaders, and the structures of FIGS. 5C and 5D include heat
spreaders below the grating structure. The structures illustrated
in FIGS. 5B and 5D further include a reflective layer below the
coupler to improve efficiency of optical coupling as described
above.
Typically the heat spreader will extend from the region below the
grating to the edge of the chip where it is in thermal contact with
the carrier that holds the chip. The contact with the carrier that
holds the chip allows for heat on the chip to be transferred off of
the chip for thermal management. In some cases the carrier has a
heat sink that is in thermal contact with the heat spreader on the
chip. In some cases, active cooling is provided to the heat sink. A
heat spreader also could be used as, or used below, an absorbing
interface instead of a reflecting interface below the grating
coupler. This can be advantageous, for example, if process
tolerances are insufficient to guarantee a desired phase
relationship between the incoming beam at the grating coupler and a
reflective layer below the bottom cladding. Where such tolerances
are insufficient, coupling efficiency can vary undesirably due to
process variation. In this case, higher absorbed heat loads would
be expected for a given coupled power, and thus a means of thermal
mitigation becomes even more critical.
For the sake of description, the terms "above" and "below" here
refer to relative position of layers for a case in which the input
beam is incident from the top of the layer stack, as commonly
described. In some embodiments, however, an inverted stack can be
used, in which case the beam is incident from below. In such a
case, a heat spreader can still be applied to laterally disperse
heat and/or aid in its extraction from the top of the layer
stack.
Example 6 below demonstrates experimentally the benefit of a heat
spreading layer in mitigating laser damage at power densities
typical of those used in the instant devices and systems.
Active Waveguide Coupling
According to another aspect, the instant specification provides
optical systems comprising an optical source and a target waveguide
device, wherein the optical energy from the optical source is
actively coupled to the target device. In traditional optical
systems containing an optical source and a target waveguide or
fiber optic device, the components are associated using either
permanent coupling or connectorized coupling. For example, in
systems where the target optical device is contained within an
integrated optical chip, is buried underground, or is strung under
the ocean in a telecommunications cable, the target device is
carefully aligned to the input source or sources (e.g., a laser
diode, an LED, or the like) and permanently fixed in place. This
process is expensive, time consuming, and usually involves glue or
other permanent adhesive. The connectorized approach is similar in
that it requires the careful alignment of a connector to the target
device. In addition, connectorized connections are usually made
manually by a human operator.
The active coupling approach described herein differs from the
conventionally coupled systems in that it involves a target
waveguide device that is readily inserted and removed from the
optical system. There is additionally a premium placed on fast
cycle times, with the target device being coupled to the optical
source as soon as possible after its insertion into the system.
Although a connectorized approach is clearly more suited for this
type of operation than a permanently coupled approach, even the
connectorized approach typically requires human intervention to
create the connection. Connectorization also adds significant cost
to the system--in the case of telecommunications systems, typically
$100 per connector.
An active coupling strategy is usefully applied to any of the
coupled systems described herein. It typically involves a laser
path that includes motorized beam steering and in some cases also
motorized focus, and it also preferably includes a feedback loop.
Simple feedback loops are described in co-owned U.S. Patent
Application No. 62/133,965 and Ser. No. 15/072,146. For example, a
waveguide tap fabricated within the target waveguide device can be
used to split out a small amount of laser power from the guided
mode, and the tapped power can be routed to a convenient location
for collection by a camera or other detector to monitor and adjust
the optical coupling through the system. Alternatively, or in
addition, light does not necessarily need to be explicitly coupled
out of the device in order to provide feedback. Instead, a camera
oriented toward a specific waveguide region can determine the
amount of light within the waveguide, in the same way that
waveguide coupling losses are estimated by quantifying the
scattering loss along the waveguide.
Another closed-loop feedback alternative for monitoring coupling is
to integrate a detector onto the waveguide itself. Although this
approach may complicate fabrication of the target device and may
increase cost (for example, a hybrid flip-chip approach is common
but expensive, and a monolithic approach requires wires), such
integrated detectors are known in the art.
For any actively coupled system, the optical source is ideally
steerable in x,y, and/or tip/tilt directions, and can additionally
be focusable. It can in certain embodiments be advantageous to
apply more sophisticated beam shaping to the optical source beam in
response to the coupling efficiency, as measured in the closed
feedback loop. Such active control over the optical input loosens
instrument tolerances on placement of the target waveguide device
within the instrument, on target device packaging tolerances and
substrate tolerances, and also on waveguide alignment tolerances
(e.g., on mask alignment). Fabrication variations in waveguide
shape and size can also be loosened by an adaptive optical input
with a closed-loop feedback. Finally, instrument drift tolerances
can be significantly loosened with closed-loop adaptive optical
coupling.
A variety of coupling methods can be used independently for
inputting an optical signal into a target waveguide device. These
methods can additionally or alternatively be used without
limitation to couple optical signals out of the device, for example
to an optical detector, detectors, or the like. The three classic
approaches to coupling include transverse or endfire coupling,
prism coupling, and grating coupling. Each of these techniques has
certain advantages with respect its use in an optical analytical
system. In particular, transverse coupling requires little or no
space on the target device and provides a high level of overall
coupling efficiency (70-90%). Transverse coupling, however,
requires polishing of the side of the target waveguide device, can
impact packaging of the device within an optical system, and can
require sensitive alignment of the target device in three
dimensions. Prism coupling also displays relatively high coupling
efficiencies (50-80%), but it requires the incorporation of a
high-index prism into the system packaging, space on the surface of
the target device, and alignment of the target device with respect
to prism tilt. Standard grating coupling efficiency can be
relatively low, but the efficiency is significantly improved (to
90%) with specific grating profiles and incident beam energy
distributions. Grating coupling also requires space on the surface
of the target device and is sensitive to tilt alignment between the
optical source and the target device.
As will be further described in the Examples, the overall coupling
efficiency of an optical system is defined as
.eta.=.eta..sub.instrument.eta..sub.target device.eta..sub.optical
source where the instrument coupling efficiency
(.eta..sub.instrument) describes the ratio of power in the guided
mode to the total power delivered to the target device by the
instrument. The denominator includes unused power that does not
couple into the target device in the form of substrate modes or
other:
.eta..times..times..times..times..times..times..times..times..times..time-
s. ##EQU00006## where the target device coupling efficiency
(.eta..sub.target device) describes the ratio of power in the
guided mode to the total power coupled into the device, and where
the denominator includes power in substrate modes which must be
prevented from reaching any detector elements:
.eta..times..times..times..times..times..times..times..times..times..time-
s..times..times..times..times. ##EQU00007## and where the optical
source efficiency describes the fraction of light coupled into a
guiding layer that can be successfully coupled into individual
channel waveguides:
.eta..times..times..times..times..times..times..times..times..times..time-
s..times..times..times..times. ##EQU00008## The values of
.eta..sub.target device and .eta..sub.optical source should
generally be considered more important than .eta..sub.instrument
within an integrated system, because they represent light scattered
inside the target waveguide device that can increase background
signals and thus put pressure on the laser rejection filters and
other background mitigation strategies. Low instrument efficiencies
can be compensated for by changes in instrument design. Exemplary
target waveguide design and estimation of coupling efficiency is
provided below in Example 2. Multimode Integrated Coupler
According to another aspect, the instant specification provides
multimode integrated optical coupling devices and optical systems
comprising such devices. As described above, target waveguide
devices typically include a limited number of optical inputs that
are coupled to an optical source. Optical energy entering the
device is directed by waveguides to locations of interest within
the device through splitters that are fabricated within "fan-out"
regions of the target device. The devices disclosed in this section
of the disclosure, however, include a multimode coupler element. In
these devices, the role of the multimode coupler element is not to
route light to individual output waveguides, but rather to
distribute the light into pre-planned "hotspots" where nanoscale
sample wells are located.
The design of the multimode coupler device allows flexibility in
the spacing, location, number, and relative brightness of the
hotspots. Multimode couplers are a mature technology with a great
deal of process development and design approaches already in place.
A photograph of an exemplary 1.times.8 splitter device is shown in
FIG. 6, where hotspots are clearly evident in an arrayed pattern
across the surface of the device. A nanowell can accordingly be
placed on top of each hotspot.
The design space of such multimode devices is quite flexible, with
devices designed to have different spacing and intensity. In
particular, in some embodiments, the devices are designed to
display more efficient use of laser power, lower propagation loss,
lower autofluorescence, allow a more flexible layout of nanowells,
and use less space on the chip for routing and/or splitting. In
some embodiments, a specified number of waveguides are fanned out
and illuminated, but the waveguides are terminated in a multimode
coupler structure. In specific embodiments, the structure is square
or rectangular, or it could be another structure that uses space
more efficiently, for example with greater packing density. The use
of a multimode coupler could partly or completely eliminate the
large cascade of splitters necessary in a fan-out region to divide
a single input waveguide into thousands or more separate waveguides
for transmitting light to the nanoscale sample wells.
In some embodiments, the multimode couplers are designed to provide
varying intensity. For example, the intensity can be programmed to
compensate for scattering loss, propagation loss, loss at the
nanowell, and the like.
In some embodiments, the devices are designed to provide
programmable excitation. Such devices are similar to classic
waveguide illumination, with optical switches implemented to switch
on and off different regions of the chip. In some embodiments, the
devices are designed to provide variable excitation. As is used in
classic waveguide illumination, variable optical attenuators (VOAs)
can be integrated into different lines to provide for adjustment of
the power density at different groups of nanowells. Such variable
excitation could be used in a "per chip SNR" optimization, where it
could be used to adjust power output after initial results from
subsections of a particular chip. It could also be used to program
the chip with a diversity of excitation powers and simultaneously
collect data at different optimization points on the laser
titration curve.
All of the above optical features could be achieved using
traditional optical trains as well as with classical waveguide
illumination approaches, but they are far simpler to achieve using
a multimode coupler device. In addition, a multimode coupler
overcomes some of the problems that can arise with traditional
optically coupled devices. For example, it is generally difficult
to space output waveguides as closely together as desired because
of interference between guided modes. Autofluroescence may also
limit the potential SNR of a classical waveguide device. The
splitters used in a classical waveguide device may additionally be
problematic in that they require significant amounts of space on
the device. Traditional splitters may also limit accuracy of the
device, as each stage adds variability into the different
branches.
Polarization Schemes for Efficient Excitation of Nanowells
According to another aspect, the instant specification provides
methods and devices for optimizing the excitation of arrayed
nanowells in an optical analytical device. As described above,
analytical reactions, preferably immobilized single template/DNA
polymerase sequencing reactions, are excited with laser light,
typically near metallic nanostructures. In such systems, the
polarization of the optical source is an important consideration in
implementing the design. In typical systems, the input light is
linearly polarized due to the properties of the optical train. In
most circumstances, however, a different polarization would be more
efficient. Higher efficiency results in better uniformity of
excitation and lower power requirements for excitation. Better
uniformity improves the quality of data generated from the
analytical reaction, and lower power requirements translates into
lower autofluorescence and lower heat generation.
In the above-described integrated target devices, the nanowells are
illuminated by an optical source within the device, typically an
excitation waveguide. The nanowells are preferably cylindrical in
shape, wherein the inner walls are commonly formed from a metallic
layer, and the bottom of the nanowell is commonly a glass/water
interface. As is known in the art, the penetration of an evanescent
electric field into a metal varies with polarization of the optical
source, and there is correspondingly a strong polarization
dependence for the evanescent fields exciting nanowells in such
devices due to the metallic layer surrounding the nanowells. When
an enzyme, such as a DNA polymerase, is immobilized at a specific
location within a nanowell, the strength of the electric field from
the optical source thus varies significantly depending on the
position of the immobilized enzyme, and thus the fluorescent target
molecule, within the nanowell.
The instant inventors have discovered that a simple linear
polarization of excitation light generally provides relatively poor
field uniformity inside a metallic nanowell, but that the
uniformity can be improved by an alternative approach to
polarization. In particular, for some systems using linearly
polarized excitation light, the falloff in excitation energy can be
a factor of two between edge locations aligned with the laser
linear polarization (0.degree. and 180.degree.), and locations
orthogonal to the polarization direction (90.degree. and
270.degree.). For example, as illustrated in FIG. 7, target
molecules positioned in a nanowell (i.e., a ZMW) at locations 1 or
2 experience high laser electric fields when excited by
linear-polarized laser light, whereas those positioned at locations
3 or 4 experience significantly lower electric fields. A graph
representing the estimated falloff in electric field along the x
and y coordinates is also shown in FIG. 7. By comparison,
circularly polarized light reduces the variability in the
excitation field by half. It should be understood that the
fluorescence signal varies quadratically with excitation electric
field, so the impact of non-uniformity in excitation field can be
significant.
As an alternative, if a nanowell is excited with circularly
polarized light, while there is still a falloff between the peak
electric field location in the center of the nanowell compared to
the edge, this falloff is radial and not as deep. Accordingly, as
shown in FIG. 8, target molecules positioned in a nanowell at
locations 1, 2, or 3 would experience similar electric fields when
excited by circularly-polarized light. It should also be noted that
other system performance metrics may be affected in different ways
by the target molecule position, and an increased uniformity of
excitation field is but one factor in improving performance of the
system. However, converting to circularly polarized light removes a
significant factor that is a function of azimuthal and radial
location within the nanowell and thus reduces overall variability
in the excitation level.
Depending on the particular optical system, the conversion of an
excitation beamlet from linear to circular polarization may be more
or less complicated. For a relatively simple case, for example
where the excitation beam is provided in a traditional optical
train, the conversion may be effected, for example, by the simple
addition of a quarter wave plate at a collimated location in the
laser path. This modification converts the light at that spot from
linear polarization to circular. The ultimate polarization at the
nanowell will be slightly different, however, due to reflections
and asymmetric filters. The design of an appropriate waveplate or
two that results in true circular polarization at the nanowell is
straightforward, however, as would be understood by one of ordinary
skill in the art, if the optical design details of the lenses and
filters in the system are known.
For a more complex and compact optical system, for example where
the optical signal is transmitted through a waveguide, and where a
metal is used, as described above, to define the excitation volume
and to provide enhancement of the laser field strengths, the field
strength may be spatially dependent on the polarization direction.
Optical waveguides are generally polarized, with two possible
orientations (TE and TM) which are orthogonal to each other. A slab
waveguide can combine TE and TM modes, such that the TE mode can be
used to propagate one laser wavelength (532 nm) and the TM mode can
be used to propagate a second wavelength (642 nm). For purposes of
the instant disclosure, however, a slab waveguide can be used to
create circular polarization, or an approximation of circular
polarization, in the waveguide. This, or an even more complex
polarization scheme, provides maximum uniformity in electric field
across all possible target molecule locations in samples
illuminated by such waveguides. FIG. 9 provides a schematic
representation of the effect of target molecule location on
excitation by different TE modes.
Furthermore, while waveguides are typically designed for
transmission of either TM or TE modes, there is a third unique mode
definition, TEM, that can be used to transmit optical energy to
arrayed nanowells in a target device. For example, a square
embedded guide with the same index in all cladding directions could
simultaneously support both TE and TM transmission, and if the
symmetry is perfect, or nearly perfect, both TE and TM will have
identical group velocities. Similarly, a TEM mode can be used for
minimal polarization anisotropy, and hybrid modes in general can be
constructed quite generally to match a desired polarization
configuration. FIG. 10 illustrates how these modes can be combined
with different group velocities to create desired electric field
patterns in a waveguide.
Multi-look and Multi-hotstart Approaches
According to yet another aspect, the instant specification provides
devices and systems for highly arrayed optical analysis in which
the target nanowells may not necessarily be illuminated
simultaneously. In other aspects, the analytical reaction occurring
within the target nanowells may not necessarily be initiated
simultaneously in all of the nanowells.
In some embodiments, the instant integrated target devices involve
a single sequencing experiment per chip, and all nanowells on the
device are illuminated simultaneously. In other embodiments,
however, only half of the nanowells are illuminated at a time. In
still other embodiments, one third, one fourth, or even fewer of
the nanowells are illuminated at a time.
In some embodiments, a single "hotstart" initiates polymerase
activity in all of the nanowells simultaneously. In other
embodiments, polymerase activity is initiated at two, three, four,
or even more times on a given target device. Initiation of
polymerase activity may be triggered in various ways, for example
by the addition of an essential component of the enzymatic
reaction, e.g., one of the four nucleotides in a DNA
polymerase-catalyzed reaction, that is initially not present in the
sample or that is initially present in limiting amounts. In some
embodiments, polymerase activity is triggered by the release of a
trapped form of an essential component or by activation of an
otherwise inactive form of the component. In these embodiments, the
essential component could be, for example, one of the four
nucleotides required for the DNA polymerase reaction, or could be
the DNA polymerase enzyme itself.
The multi-look and multi-hotstart concepts disclosed herein address
some of the challenges in the use of integrated waveguide devices
for the measurement of nanoscale analytical reactions. For example,
autofluorescence in the waveguide core material, laser scattering
light levels combined with limited design space for laser blocking
filters, heating of the coupling pad due to imperfect coupling
efficiency, and large laser power required can be problematic.
Independent of the waveguide illumination scheme, the compute
bandwidth is an important engineering problem. The figure of merit
for all of these issues is divided by the number of looks in a
multi-look approach (e.g., if a 10 W laser is required for single
look, 5 W would be required for two-look; if the autofluorescence
level is X in a single look, it would be X/2 in a two-look, and so
on). Although the use of multi-look approaches decreases instrument
throughput, it can also reduce the cost per analytical reaction of
the device and can also simplify/reduce the cost of the
instrument.
In terms of waveguide illumination, there are several ways to
implement multi-look excitation. An instrument-centric approach is
to include multiple optical inputs on the target waveguide device,
and aim an input optical beam at one of these inputs at a time.
FIG. 11 illustrates how this approach could be implemented with two
basic coupling schemes. Specifically, FIG. 11A compares the
single-look design (top) and a 3-look variant (bottom) in a target
waveguide device containing grating couplers. With the 3-look
variant, a single input optical beam is aimed at the three separate
input grating couplers in sequence in order to excite samples along
the "Look 1", "Look 2", and "Look 3" waveguides, respectively. FIG.
11B shows the corresponding single-look (top) and 3-look (bottom)
design variants for target devices employing endfire coupling. The
corresponding designs for target devices employing prism coupling
are not shown but would be similar to the designs shown for the
grating-coupler devices of FIG. 11A. Specifically, in the
prism-coupled devices, the input grating couplers of the designs
shown in FIG. 11A would be replaced with input prism couplers.
A further example of the multi-look approach, in particular where
the instrument provides multiple optical beams for illumination of
a target device, is illustrated graphically in FIG. 12. A
single-look device with input grating couplers and designed for use
with three input optical beams is shown in FIG. 12A. A
corresponding 3-look device with input grating couplers and
designed for use with three input optical beams is shown in FIG.
12B. In each case, the three input beams are indicated in the
drawing as ovals positioned to the left of the respective devices.
It should be understood, however, that these beams would, in
practice, illuminate the input couplers on the devices and be
launched into the integrated optical waveguides in each case.
Similar designs could be prepared using prism input couplers in
place of the grating input couplers. FIG. 12C shows a 3-look
endfire-coupled device for use with three input beams. The input
beams in this device are designated by the three pairs of
convergent lines targeting the waveguides. In FIGS. 12B and 12C,
movement of the three input beams from look to look is indicated by
small arrows.
A variety of on-chip optical switches are also available for
implementing the multilook concept. An efficient and inexpensive
example is a thermally-activated Mach-Zehnder switch. Since these
switches are relatively slow and display different on/off speeds,
they are most suitable in instruments where switching times of one
or two seconds are sufficient. It should also be noted that on-chip
switching is independent of the coupling scheme. An endfire-coupled
target device with a single optical input is illustrated in FIG.
13, but corresponding grating-coupled and/or prism-coupled target
devices could likewise be designed. As shown in the device of FIG.
13, three Mach-Zehnder switches are used to control the excitation
of four different waveguides to provide four separate "looks" in
this device. A more detailed view of an individual thermal
Mach-Zehnder switch is also shown in FIG. 13. Such switches are
known in the art and can be readily included in the design and
fabrication of an integrated waveguide device.
Polarization can also be used to implement a two-look scheme. The
use of polarization can advantageously require fewer moving parts
or smaller adjustment ranges in the instrument, and less real
estate than an on-chip version. An instrument-level implementation
of such an approach is depicted in FIG. 14A, and an on-chip
implementation is depicted in FIG. 14B. Specifically, the target
device shown in FIG. 14A includes a polarization-sensitive beam
splitter that is used to route light between two different
waveguides ("Look 1" and "Look 2"). The optical input is switched
by the instrument between polarization states (e.g., s and p) for
recognition by the beam splitter. The target device shown in FIG.
14B includes a polarization-maintaining input waveguide that leads
to a degenerate guide. A Pockels cell polarization switch, or the
like, is used to modulate the polarization state of light passing
through the device, and a downstream polarization-sensitive beam
splitter routes light between two different waveguides ("Look 1"
and "Look 2") for transmission to the respective nanoscale sample
wells.
Wavelength tuning can also be used for implementing the multilook
concept. In this approach the laser in the instrument is a tunable
laser, and the optical input is routed through the device according
to the wavelength. A basic arrayed waveguide grating (AWG) device
could be used here, with a large number of looks enabled according
to established AWG technology. An exemplary AWG-implemented target
device with six output waveguides is shown in FIG. 15. Note that
the excitation source could be tuned, for example in 25 nm
increments, with each increment being directed to a different
"Look". Alternatively, a broadband source (e.g., an LED) could be
used along with a tunable filter that would select one wavelength
at a time. The wavelength step size should be chosen to be small
enough that the differences would not have a significant impact on
excitation of the subject analytical reaction.
Fiber Spacing Concentrators and Fiber Alignment
According to yet another aspect, the instant specification provides
fiber spacing concentrators with reduced loss and improved
channel-to-channel uniformity.
Multi-channel microfabricated optical devices are of use in
telecommunications applications, for high-speed optical
interconnects in computing, and potentially for bioanalytical
applications. Optical fibers are typically used to transmit signals
at the macro scale, and various means can be used to couple the
signal between a microfabricated structure and an optical fiber.
However, there is a large mismatch between the minimum pitch of
coupling structures on a microfabricated component (which
structures can be roughly the size of the optical fiber mode and
thus spaced on this scale) and the minimum pitch of an array of
optical fibers (limited by the fiber cladding or coating diameters,
which can be 30.times. the mode diameter or more). From a practical
standpoint, this means that more area--and thus more cost--must be
devoted to coupling structures on the chip than required from an
optical perspective.
A fiber spacing concentrator (FSC) is a planar microfabricated
passive optical component used to provide well-defined spacing of
multiple individual optical channels with a fixed pitch that can be
made much tighter than the spacing between optical fibers in a
fiber array. Embodiments of such FSCs are available commercially.
See, e.g., fiber spacing concentrators from Teem Photonics, Meylan,
France
(http://www.teem-photonics.com/fiber-spacing-concentrator.html).
Use of an FSC for optical coupling allows for much tighter spacing
of couplers on the target microfabricated optical device, thus
reducing the required area and cost for a given number of channels.
However, this benefit comes at the cost of some loss of optical
transmission, which can be non-uniform across the array. Additional
power and potentially additional degrees of freedom for power
control can be required to compensate for such non-uniform losses,
which ultimately add to system cost.
From a physical perspective, the FSC consists of three key
components: a microfabricated part in which waveguides are defined,
a mechanical assembly for holding an array of fibers, and the fiber
array itself. The fiber array can be fixed (e.g., bonded) in the
mechanical assembly before subsequent alignment of the mechanical
assembly and bonding to the waveguide component.
A large fraction of the losses in an FSC assembly likely arise from
the spatial mismatch between the waveguide structures in the
microfabricated component and the locations of the cores of the
individual fibers in the array. While the main component of the FSC
is lithographically patterned to nanometer-scale accuracy, the
array of spots from the fiber array is mechanically defined. Errors
in spot position can arise from manufacturing tolerances in the
array of V-grooves used to hold the fibers, which can be sub-micron
for a part also made lithographically, as well as from
core-cladding concentricity errors of the individual fibers, which
can be substantial on the scale of the spot diameter (e.g. 1 .mu.m
concentricity error with 3.4 .mu.m mode field diameter for a
single-mode fiber in a visible wavelength). Exemplary V-groove
assemblies, and their alternatives, are described in U.S. Pat. No.
7,058,275.
To reduce the loss of optical throughput in the FSC, as well as to
improve uniformity among channels in the FSC, it would be
advantageous to better control the spacing of the fiber modes at
the interface between the fiber array and the waveguide structure.
This might be done with active control of individual fiber position
at assembly, but the challenges of simultaneously fixturing many
small fibers for active alignment and subsequent bonding in place
in a very restricted volume (with fiber spacing on the order of the
fiber diameter) are difficult.
To improve uniformity and reduce losses in an FSC assembly, the
bare fibers in the mechanical assembly (for example in a V-groove
array) can be replaced with pre-aligned fiber and ferrule
assemblies that can offer much tighter concentricity. See FIG. 16.
Active alignment of individual fibers to ferrules is an existing
process capable of providing very low loss in fiber-to-fiber links.
Concentricity tolerances can be reduced from .about.1 .mu.m for
bare fiber to .about.125 nm between the core and a
precision-polished ferrule. Suitable ferrules and core alignment
technologies are available commercially, for example, from Diamond
SA, Losone, Switzerland. This approach substantially reduces the
overall alignment error between fiber core and waveguides in the
FSC, resulting in improved uniformity and lower transmission
losses.
Various aspects of the devices can be varied including: The
operating wavelength, fiber mode field diameter, and type. Number
of inputs to the FSC--this approach is readily applicable to an FSC
with arbitrary channel count. Details of the active alignment
technique for individual inputs in the FSC. Commercial products are
available with a pre-aligned ferrules that are readily incorporated
into an integrated solution with only minor changes to V-groove
geometry/spacing. Design of the microfabricated portion of the FSC.
Removal of the microfabricated portion of the FSC, leaving the
V-groove array with pre-aligned fibers. This alternative provides
an accurately spaced array of spots on a large pitch for any
application where it is appropriate. Materials of the V-groove
array (glass or silicon or otherwise), and methods of assembly
(e.g., adhesive bonding or mechanical fastening).
Fiber spacing concentrators are available commercially, where
losses are on the order of 1 dB for applications in typical telecom
wavelengths in the near IR. Losses would increase for visible
wavelengths using existing devices, as the sensitivity to a given
degree of mechanical misalignment increases with decreasing spot
size/MFD. The approaches described here improve the throughput
losses and non-uniformity of existing FSCs.
According to yet another aspect, the instant specification further
provides innovative approaches to the alignment and connection of
optical fibers. In particular, these approaches relate to the use
of an active actuator to complete the interconnection. Such
approaches can be low cost and easy to use.
As is known, low power and low power density fiber modes can be
effectively coupled through precision ferrules and passive mating
sleeves. High power, high power density, and small mode field
diameter fibers are more challenging for passive interconnection,
however, owing both to risk of damage from contamination and tight
tolerances.
Passive free space interconnects have been used in order to couple
with low risk of damage. These interconnects are, however,
typically expensive and time consuming to use. Passive physical
contact interconnections are well known for telecommunication
applications. The physical contact interconnects are not well
suited for high power visible light applications, for which even
minute contamination can lead to a runaway that causes destruction
of the fiber (aka fiber fuse), or may result in less catastrophic
but still substantial reductions in transmission.
High power fibers use end caps, a fused unguided section to expand
the mode and increase the threshold against damage from
contamination. Unfortunately, this end cap also precludes the use
of efficient physical contact connectors for the same reason.
Free space interconnections for fibers with end caps are available
commercially. Such devices can be based, for example, on mechanical
actuation driven by manual lead screws. The aligned optic can be,
for example, a pair of mirrors. While such approaches can be
effective, they are expensive and require skilled labor time to
align at each fiber insertion.
An alternative is the use of an active optical element to match the
expanded modes between two such single mode devices. This can make
use of optics to create multiple beams to guide the alignment
(e.g., diffractive optical elements (DOEs)) or other servo
features. A device such as the Varioptic Baltic 617 or similar can
be effective in matching modes to ensure an efficient, low cost
interconnect with good tolerance to contamination.
The active optical device can be based on different actuation
methods (EAP, VCM, PZTs, etc.). The device can be based on scanning
prisms (e.g., Risley pair), though these may be more costly.
Methods based on diffraction gratings, real time or not, can also
be used.
Integrated System-On-Chip
In another aspect, the instant specification provides waveguide
devices that include an integrated optical source, where the
optical source is either fabricated within the waveguide device
itself or is attached to the device after fabrication. The
previously described optical analytical systems typically comprise
an optical source (or sources) (e.g., a PLC) that is physically
separate from the target waveguide device. Optical energy emitted
from the source is therefore coupled to the target device through
free space, as described in detail above. In some circumstances,
however, it may be advantageous for the optical source to be
integrated into the target device package, for example using a
multichip module or system in a package (SIP) approach. Such
approaches are well known in the electronics industry but have not
previously been applied to integrated waveguide devices such as
those used in multiplexed DNA sequencing chips. By integrating a
laser, or other suitable optical source, directly into the chip
package, each cell becomes a self-contained optical bench capable
of illuminating and viewing target molecules within an array of
optically coupled nanowells.
Conventional SIP approaches can accordingly be adapted for use in
the instant integrated systems, for example by modifying a
waveguide device using flip-chip assembly techniques, or the like,
for example to mount a laser diode chip or other compact optical
source directly on the waveguide device. Flip-chip bonding
techniques have been used extensively in the electronics industry,
including their more recent application to optoelectronics
components. See, e.g., Han et al. (1998) J. Electron. Mater.
27:985; Li et al. (2004) P. Elecr. C. 2:1925. Advantageously,
flip-chip techniques can make use of solder bumps for mounting
components on interconnects. Solder bumps may, upon reflowing, pull
the components into position due to the surface tension of the
molten solder, thus facilitating the alignment of optical
components during assembly. The choice of optical source will
depend on the needs of the system. Although traditional laser
diodes are edge emitters and may therefore require more complex
assembly arrangements, newer technologies, such as, for example,
vertical cavity surface emitting laser (VCSEL) technologies, enable
more direct optical coupling from the source to the waveguide
device.
It will be readily apparent to one of ordinary skill in the
relevant arts that other suitable modifications and adaptations to
the devices and systems described herein can be made without
departing from the scope of the invention or any embodiment
thereof. Having now described the present invention in detail, the
same will be more clearly understood by reference to the following
Examples, which are included herewith for purposes of illustration
only and are not intended to be limiting of the invention.
EXAMPLES
Example 1
Binary Grating Couplers with Low Numerical Aperture
This example describes the design, optimization, and modeling of
various binary grating couplers having low NA. The coupling of
optical energy through free space to a 2-dimensional grating
coupler can be modeled using finite-difference time-domain (FDTD)
numerical analysis of the Maxwell equations, for example using
computer software from Lumerical (www.lumerical.com) or the like.
An example of such modeling is shown in FIG. 17A, where the
2-dimensional Gaussian light source (1702) is shown in light
shading above the device model. The arrow shown within the light
source represents a coupling angle of 10 degrees. The arrow is
shown intersecting a rectangular box that represents the grating
coupler structure (1704). The oxide cladding (1706) is the solid
layer surrounding the coupler. The waveguide core (1708) is
represented as a thin line extending to the left from the coupler.
Optical energy is coupled from above the structure through the
grating coupler into the waveguide core. FIG. 17B shows the results
of the FDTD simulation, showing the light (in power units) coupling
through the grating and propagating to the left down the waveguide
core.
FIG. 18 summarizes the structural features of various binary
grating coupler designs and compares the FDTD-modeled coupling
efficiencies for those designs. The designs correspond to those
described in FIGS. 3C-F. FIG. 19 shows the results of FDTD modeling
of grating couplers having structures corresponding to that of FIG.
3A with different numerical apertures (NA). Beam sizes and grating
sizes were varied in the models to be consistent with the numerical
apertures.
FIG. 20 illustrates the impact of numerical aperture on the
alignment tolerances for beam and grating pairs. As is clear from
the models, the efficiency of coupling for the low NA couplers is
much less sensitive to alignment between the optical source and the
grating coupler compared to coupling for the high NA couplers.
FIG. 21 compares the modeled effects of grating period (A), buried
oxide thickness (B), duty cycle (C), and etch depth (D) on
efficiency of coupling. As shown in FIG. 21A, the coupling
efficiency is sensitive to changes in the grating coupler period,
and when the numerical aperture is decreased, the coupling
efficiency becomes even more sensitive to variations in the period.
Since the period is mainly determined by the accuracy of
lithography and masking during chip fabrication, however, these
variations can be well controlled. It should also be noted that the
sensitivity of coupling efficiency on period also shows angular
tolerance. Smaller numerical apertures correspond to tighter
angular tolerance.
FIG. 21B demonstrates that coupling efficiency is very dependent on
the thickness of the bottom oxide cladding. This dependence on
bottom oxide cladding thickness is observed at all values of
numerical aperture. Without intending to be bound by theory, it is
believed that this dependence results from reflection of optical
energy from the silicon substrate.
FIG. 21C shows that coupling efficiency is relatively insensitive
to changes of grating coupler duty cycle for couplers with high
numerical aperture, but the coupling efficiency becomes more
sensitive to changes in duty cycle as the numerical aperture is
decreased. Likewise, as shown in FIG. 21D, coupling efficiency is
relatively insensitive to changes of grating coupler etch depth at
high numerical aperture, but the sensitivity to etch depth
variation increases for lower numerical apertures.
FIG. 22 summarizes simulations for couplers designed using
parameters obtained from the simulations of FIG. 19. The bottom
three rows show results using these parameters in simulations using
an etch depth of 115 nm. The optimal bottom oxide thicknesses are
as shown in the bottom row of the figure.
Example 2
Estimation of Coupling Efficiencies into Model Target Waveguide
Device
This example provides estimated coupling efficiencies for a
waveguide device with an Si.sub.3N.sub.4 core with dimensions
roughly 0.600.times.0.050 .mu.m, surrounded by SiO.sub.2 cladding,
and supporting a single TM.sub.0 mode.
Coupling efficiency:
.eta..times..times..times..times..times..times..times..times..times..time-
s..times..times..times..times. ##EQU00009## Waveguide effective
index:
.beta. ##EQU00010## .lamda.=532 nm, k=1.18.times.10.sup.-9
cm.sup.-1 .beta.=1.87.times.10.sup.5 cm.sup.-1 .kappa.=coupling
coefficient (mode overlap integral) Maximum condition:
.kappa.L=.pi./2 Requirement for minimum radius of curvature: 0.9 mm
Radiative loss per bend: 0.5 dB
A not-to-scale representation of the exemplary waveguide
cross-section is shown in FIG. 23A. Estimates of coupling
efficiency are based on a calculation of the overlap integral
between the desired mode profile and the excitation field. An
analytics solution of the fields for this geometry is not known,
but the basic mode profile of the TE.sub.0 mode of this waveguide
can be approximated (Schlosser and Unger, based on assumption of
large aspect ratio). The electric field intensity through the
center of the waveguide is plotted in FIG. 23B (Schlosser
approximation).
Example 3
Theoretical Transverse Coupling into Waveguide Device with a
Polished Facet
The overall coupling efficiency of a device with a polished facet
is the product of reflectance loss and mode overlap, where
reflection loss for free-space coupling is larger than for an
incident plane wave: 9.6%. Perfect coupling would require an
incident energy distribution that is exactly the inverse of the
far-field distribution of light exiting the guide. A more accurate
calculation of the reflectance loss, however, would require
integration over these angles. The result of integrating over the
high NA dimension only is 12.4%. The best-case insertion loss of
the device under a straightforward approach is
.eta..sub.instrument=0.876 The efficiency could be improved by
applying an AR coating. The efficiency could also be improved by
including a very small air gap--on the order of the light
wavelength--between the target device and the exit facet of the
illumination source.
Efficiencies are determined by the mode overlap integral:
.eta..intg..intg..function..times..function..times..times..times..times..-
times..times..times..intg..function..times..function..times..times..times.-
.times..intg..function..times..function..times..times..times..times..times-
..times..times. ##EQU00011## Simulations for prototype coupled
waveguide devices are shown in FIG. 24, where the left panel shows
a mode profile for a simple channel guide, and the right panel
shows the same channel guide with an added nanohole is added. A
small perturbation to the field profile is noticeable at the center
top edge, but this perturbation was ignored for coupling
estimates.
In principle, an input optical beam can be created with very good
match to the mode profile. As a limiting case, it can be assumed
that the overlap integral is perfect for perfect alignment. In this
case the sensitivity to alignment can be estimated by a calculation
of the overlap integral as a function of beam displacement. Since
the degree of confinement in the y direction is much stronger than
in x, only y misalignment can be considered. Specifically, the
spatial scale of y misalignment impact is roughly 5.times. larger
than for x misalignment, and it is easier to mitigate with in-plane
tapering of the guide input section.
The impact of y misalignment is calculated from the mode overlap
integral and illustrated in FIG. 25. At 100 nm misalignment, the
power drops by roughly half. If high device efficiency is needed,
or if a low drift in intensity at measurement locations on the
target device is needed, active alignment may be necessary. It may
also be worth considering increasing the beam size in order to
loosen the mechanical requirements for achieving a certain minimal
field intensity at the measurement locations on the target device,
but an increased beam size will not change the ratio below, nor
will it change the tolerance on a given power stability
requirement. A flattop intensity profile could be considered; in
such a configuration a gradual drop in intensity is avoided at the
expense of a rapid falloff at the edge of a "safe" range.
Example 4
Theoretical Coupling into Waveguide Device Using a Prism
Coupler
An optical waveguide confines light in the x and y dimensions; the
confinement requires total internal reflection and a cladding with
lower index than the core. Coupling into a target waveguide device
by simple refraction is not possible. The geometry of coupling is
constrained by phase-matching between the free-space optical source
beam and the guided mode according to:
.beta..times..pi..times..times..lamda..times..times..times..theta.
##EQU00012## Assuming a perfectly collimated input beam with
diameter W, .theta..sub.m is the incident angle of the input beam
inside the prism. The coupling coefficient, .kappa., is determined
by mode overlap similar to the description in Example 2. The
coupling efficiency, .eta., is determined by .kappa. and the
interaction length, L. Finally, weakly coupled modes are
assumed.
It is theoretically possible to achieve 100% coupling efficiency in
this arrangement with a perfectly controlled air gap and waveguide
tolerances and with a flattop incident beam. In practice, however,
coupling efficiencies of 90% have been demonstrated in the
laboratory. Such efficiencies have required a non-Gaussian beam and
a tapered air gap. In a straightforward approach with a uniform air
gap and a Gaussian beam, efficiencies very close to the 81%
theoretical limit have been demonstrated. The tolerances required
for this approach in this example are as follows: Air gap: 30 nm
Air gap variation=0 z alignment accuracy: 50 nm y alignment
accuracy: 50 nm* cos .theta..sub.m. For perfect geometry complete
coupling occurs at an interaction length,
.times..times..theta..pi..times..kappa. ##EQU00013##
It should be understood that misalignment in the z direction will
prevent complete coupling. Furthermore, complete coupling can only
occur for a flattop beam, whereas a Gaussian beam is theoretically
limited to 80% efficiency, even for a perfect geometry. If the
efficiency requirement is relaxed to 60%, the tolerances become
much looser. Accordingly, for the instant example,
.eta..sub.instrument.eta..sub.device=0.6, with
.eta..sub.device=0.80.
It has been noted that the prism must have a higher refractive
index than the cladding material. This requirement is very general,
but maximum coupling efficiencies and instrument configurations are
dependent on the prism index selected. A higher index implies a
lower incident angle, which is convenient for flexibility in
instrument and device packaging, and higher theoretical coupling
efficiencies. For example, FIG. 26 illustrates the relationship
between prism refractive index and the input incident angle for a
prism-coupled device, where the effective refractive index of the
device is 1.58.
Example 5
Theoretical Coupling into Waveguide Device Using a Grating
Coupler
The efficiency of a grating-coupled target device is fundamentally
lower than for a transverse-coupled or prism-coupled
device--typically 10% for a simple grating structure.
Significantly, a grating coupler lacks the chief advantage of prism
coupling, which allows the incident energy to be largely confined
to a single mode. In particular, zero order energy passes directly
into the substrate with a grating coupler, as do many of the
nonzero orders. Additionally, no total internal reflectance means
strong coupling, each waveguide mode has a complete set of spatial
harmonics underneath the grating, and the grating itself has higher
orders. The efficiency of a grating coupler can be improved by
fabricating complicated grating profiles. For example, high
efficiency can be put into one order to improve the coupling.
Furthermore, the z and y mechanical tolerances are very similar to
the prism coupling case, with the difference being that light is
more quickly coupled into substrate modes in the grating case as
the beam is misaligned.
The basic phase-matching condition for a grating of period d is
.beta..times..pi..lamda..times..times..times..theta..times..pi.
##EQU00014## Phase-matching can be achieved over a wide range of
angles and grating periods, so strictly speaking there is
flexibility in choice of grating period. Instrument considerations
argue for larger incident angles, however, whereas target device
space considerations argue for smaller incident angles. FIG. 27
illustrates the relationship between the grating period and the
input incident angle for a device of this example, where the
effective refractive index of the device is 1.58.
TABLE-US-00002 TABLE 2 Summary of the best-case coupling parameters
for three exemplary coupling approaches. Transverse Prism Grating
.eta..sub.device 1.0 0.80 .eta..sub.optical source 0.68 0.68 0.68
.eta..sub.instrument 0.88 0.96 y misalignment (3 dB) 110 nm X
misalignment (3 dB) 670 nm
Example 6
Laser-Induced Damage Due to Heating on a Target Waveguide
Device
As described above, target waveguide devices may be susceptible to
thermal damage due to the high intensities of excitation energy
needed to illuminate the large numbers of nanoscale reactions being
analyzed in a high-density waveguide array. This example
demonstrates the protective effect of including a heat spreading
layer within the target device.
FIG. 28 illustrates the test setup and shows the power densities of
lasers with various numerical apertures. As is apparent in this
figure, even with a low numerical aperture (e.g, 0.01) and large
beam size (e.g., 33.87 .mu.m), a 100 mW laser will still have a
relatively high power density (e.g., 1.11.times.10.sup.4
W/cm.sup.2). The power densities used in the test setup were
therefore chosen to simulate this range (e.g., 5 to 780 mW laser
power; corresponding to 1.38.times.10.sup.2 to 2.15.times.10.sup.4
W/cm.sup.2). The figure also illustrates from below and in
cross-section the sample used in these tests. Specifically, the Si
substrate was coated with a 2 .mu.m layer of SiO.sub.2, a 0.5 .mu.m
layer of amorphous Si, another 2 .mu.m layer of SiO.sub.2, and
finally a 100 nm layer of Al. The sample also included 8 windows
etched through the Si layer. For reference, the thermal
conductivities of SiO.sub.2, Si, and Al are 1.4, 149, and 240,
respectively.
Both surfaces of the samples were visually inspected under a
microscope prior to illumination with various intensities of laser
energy. In the first experiment, the laser was directed through the
window in the Si layer to target the SiO.sub.2 layer, as indicated
by the arrow the structural diagram of FIG. 29A. Illuminating the
sample for 5 minutes at either 5 mW of power or 50 mW of power
caused no damage, but the sample was instantly damaged upon
illumination with 100 mW of laser power. The SiO.sub.2 sides of the
three samples are shown in the top row of FIG. 29B, and the damage
to the Al side of the 100 mW sample is shown in the bottom row of
the figure. In the second experiment, the laser was directed to the
Al side of the sample in the region of the etched window, as
indicated by the arrow in the structural diagram of FIG. 29C. In
this experiment, a 5 minute illumination at 100 mW laser power
caused no damage, whereas damage was observed instantly at 500 mW
laser power. These samples are shown in FIG. 29D. A third
experiment was similar to the second, where the laser was directed
to the Al side of the sample in the region of an etched window, as
indicated by the arrow in the structural diagram of FIG. 29E. Laser
outputs of 200 mW, 300 mW, and 400 mW were applied to the sample
with no visible damage. Illumination of the same with 450 mW of
laser power, however, resulted in damage within 3 seconds. This
sample is shown in FIG. 29F. A final experiment was run, where the
Al side of the sample was illuminated by the laser in a region at a
distance from a window through the Si substrate, as indicated by
the arrow in the structural diagram of FIG. 29G. In this
experiment, no damage was observed at either 500 mW or 780 mW laser
power.
Example 7
Simulation of Optimal Waveguide Dimensions for Single-Mode
Operation
FIG. 30 shows a simulation of waveguide dimensions meeting
single-mode conditions for two different core materials (SiN, top;
TiO, bottom) at 552 nm. The upper left and lower right insets show
FDTD simulation results for a thin and wide waveguide and a thick
and narrow waveguide, respectively. The Lumerical 2D simulation
setup is illustrated in FIG. 32A, and the power coupling simulation
results are shown in FIG. 32B.
Example 8
Simulation of Grating Coupler Designs with Titanium Oxide Core
A grating coupler with a titanium oxide core and high numerical
aperture (NA=0.13) but otherwise similar in design to the grating
coupler described in Example 1 and modeled in FIG. 17A has been
simulated by FDTD numerical analysis at two wavelengths. The input
beam (at either 532 nm or 552 nm) has a beam waist of 1.75 .mu.m
(beam MFD=3.5 .mu.m), a source size of 7 .mu.m, and a fiber
coupling angle of 10 degrees (with no angle tuning during the
optimizations). The Gaussian profile for the input beam is
illustrated in FIG. 31. Geometrical, mechanical, and optical
specifications for a corresponding single-mode fiber (460 HP) are
available, for example, from Thorlabs, Inc., Newton, N.J., USA
(www.thorlabs.us). The setup for the FDTD 2D simulation using
Lumerical software is shown in FIG. 32A, and the simulated power
coupling results are shown in FIG. 32B.
Modeling of the coupling efficiency for a high NA grating coupler
center design with a titanium dioxide waveguide core at various
wavelengths of input light is shown in FIG. 33. In this simulation,
the coupler was modeled using the parameters listed in the second
column of Table 3.
TABLE-US-00003 TABLE 3 High NA grating coupler center design
features for simulations at 552 nm and 532 nm. Parameters for
Parameters for 552 nm simulations 532 nm simulations Waveguide core
TiO.sub.2 (n = 2.55) TiO.sub.2 (n = 2.55) Waveguide cladding
SiO.sub.2 (n = 1.46) SiO.sub.2 (n = 1.46) Waveguide thickness 100
nm 100 nm Grating coupler number of 20 20 periods Al reflector
thickness 100 nm 100 nm Top cladding thickness 220 nm 200 nm
Grating coupler period 315 nm 300 nm Grating coupler teeth width
157 nm (duty 150 nm (duty cycle = 50%) cycle = 50%) Grating coupler
etch depth 55 nm 55 nm Reflector distance 320 nm 290 nm Optimal
coupling efficiency 78.4% (-1.06 dB) 78% (-1.08 dB) Fiber x
position 1.6 .mu.m 1.8 .mu.m Fiber y position 1.2 .mu.m 2 .mu.m
FIG. 34A illustrates the relationship between coupling efficiency
and the grating coupler period at an input wavelength of 552 nm,
and FIG. 34B illustrates changes in coupling efficiency as a
function of grating coupler period and input wavelength for the
simulated design.
FIG. 35A illustrates the relationship between coupling efficiency
and the grating coupler duty cycle at an input wavelength of 552
nm, and FIG. 35B illustrates changes in coupling efficiency as a
function of grating coupler duty cycle and input wavelength for the
simulated design.
FIG. 36A illustrates the relationship between coupling efficiency
and the grating coupler etch depth at an input wavelength of 552
nm, and FIG. 36B illustrates changes in coupling efficiency as a
function of grating coupler etch depth and input wavelength for the
simulated design.
FIG. 37A illustrates the relationship between coupling efficiency
and the reflector distance at an input wavelength of 552 nm, and
FIG. 37B illustrates changes in coupling efficiency as a function
of reflector distance and input wavelength for the simulated
design.
FIG. 38A illustrates the relationship between coupling efficiency
and the top cladding thickness at an input wavelength of 552 nm,
and FIG. 38B illustrates changes in coupling efficiency as a
function of top cladding thickness and input wavelength for the
simulated design.
FIG. 39A illustrates the relationship between coupling efficiency
and the waveguide core refractive index at an input wavelength of
552 nm, and FIG. 39B illustrates changes in coupling efficiency as
a function of waveguide core refractive index and input wavelength
for the simulated design.
Modeling of the coupling efficiency for a high NA grating coupler
center design with a titanium dioxide waveguide core using 532 nm
input light is shown in FIG. 40. In this simulation, the coupler
was modeled using the parameters listed in the third column of
Table 3.
FIG. 41A illustrates the relationship between coupling efficiency
and the grating coupler period at an input wavelength of 532 nm,
and FIG. 41B illustrates changes in coupling efficiency as a
function of grating coupler period and input wavelength for the
simulated design.
FIG. 42A illustrates the relationship between coupling efficiency
and the grating coupler duty cycle at an input wavelength of 532
nm, and FIG. 42B illustrates changes in coupling efficiency as a
function of grating coupler duty cycle and input wavelength for the
simulated design.
FIG. 43A illustrates the relationship between coupling efficiency
and the grating coupler etch depth at an input wavelength of 532
nm, and FIG. 43B illustrates changes in coupling efficiency as a
function of grating coupler etch depth and input wavelength for the
simulated design.
FIG. 44A illustrates the relationship between coupling efficiency
and the reflector distance at an input wavelength of 532 nm, and
FIG. 44B illustrates changes in coupling efficiency as a function
of reflector distance and input wavelength for the simulated
design.
FIG. 45A illustrates the relationship between coupling efficiency
and the top cladding thickness at an input wavelength of 532 nm,
and FIG. 45B illustrates changes in coupling efficiency as a
function of top cladding thickness and input wavelength for the
simulated design.
The above simulations demonstrate that grating couplers having
waveguide cores with relatively higher refractive indices (e.g.,
n.sub.core.gtoreq.about 1.9) are suitable for the efficient
coupling of an input light beam into a target waveguide device at
wavelengths above 532 nm. In particular, the design features of the
grating couplers in such target devices can be modulated in in
order to maximize coupling efficiencies of optical beams with
wavelengths where fluorescent DNA sequencing reagents have maximal
absorbance (e.g., about 552 nm). The simulations can also be
performed using input beams and input grating couplers having lower
NA values, as would be understood by those of ordinary skill in the
art.
All patents, patent publications, and other published references
mentioned herein are hereby incorporated by reference in their
entireties as if each had been individually and specifically
incorporated by reference herein.
While specific examples have been provided, the above description
is illustrative and not restrictive. Any one or more of the
features of the previously described embodiments can be combined in
any manner with one or more features of any other embodiments in
the present invention. Furthermore, many variations of the
invention will become apparent to those skilled in the art upon
review of the specification. The scope of the invention should,
therefore, be determined by reference to the appended claims, along
with their full scope of equivalents.
* * * * *
References